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P41229

- KDM5C_HUMAN

UniProt

P41229 - KDM5C_HUMAN

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Protein

Lysine-specific demethylase 5C

Gene

KDM5C

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 By similarity.By similarity3 Publications

Cofactori

Alpha-ketoglutarate.1 Publication
Binds 1 Fe2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi514 – 5141Iron; catalyticPROSITE-ProRule annotation
Metal bindingi517 – 5171Iron; catalyticPROSITE-ProRule annotation
Metal bindingi602 – 6021Iron; catalyticPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri326 – 37247PHD-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1187 – 124862PHD-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. histone demethylase activity (H3-K4 specific) Source: MGI
  3. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: InterPro
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. histone H3-K4 demethylation Source: MGI
  2. negative regulation of transcription, DNA-templated Source: UniProtKB
  3. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase, Repressor

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 5C (EC:1.14.11.-)
Alternative name(s):
Histone demethylase JARID1C
Jumonji/ARID domain-containing protein 1C
Protein SmcX
Protein Xe169
Gene namesi
Name:KDM5C
Synonyms:DXS1272E, JARID1C, SMCX, XE169
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome X

Organism-specific databases

HGNCiHGNC:11114. KDM5C.

Subcellular locationi

Nucleus 1 PublicationPROSITE-ProRule annotation

GO - Cellular componenti

  1. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ) [MIM:300534]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXSCJ patients manifest mental retardation associated with variable features such as slowly progressive spastic paraplegia, seizures, facial dysmorphism.3 Publications
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti87 – 871D → G in MRXSCJ; no effect on subcellular location and enzymatic activity. 1 Publication
VAR_032986
Natural varianti388 – 3881A → P in MRXSCJ; impairs enzymatic activity and binding to H3-K9Me3. 1 Publication
VAR_022730
Natural varianti402 – 4021D → Y in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_022731
Natural varianti451 – 4511S → R in MRXSCJ. 1 Publication
VAR_032987
Natural varianti642 – 6421F → L in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_032988
Natural varianti698 – 6981E → K in MRXSCJ; abolishes function in vivo, but no effect on enzymatic activity or binding to H3-K9Me3. 1 Publication
VAR_022732
Natural varianti731 – 7311L → F in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_022733
Natural varianti750 – 7501R → W in MRXSCJ. 1 Publication
VAR_032989
Natural varianti751 – 7511Y → C in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_032990

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi514 – 5141H → A: Abolishes enzymatic activity. 2 Publications

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

MIMi300534. phenotype.
Orphaneti85279. Syndromic X-linked intellectual disability due to JARID1C mutation.
PharmGKBiPA35964.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15601560Lysine-specific demethylase 5CPRO_0000200586Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei317 – 3171Phosphoserine1 Publication
Modified residuei1359 – 13591Phosphoserine4 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP41229.
PaxDbiP41229.
PRIDEiP41229.

PTM databases

PhosphoSiteiP41229.

Expressioni

Tissue specificityi

Expressed in all tissues examined. Highest levels found in brain and skeletal muscle.1 Publication

Gene expression databases

BgeeiP41229.
CleanExiHS_JARID1C.
ExpressionAtlasiP41229. baseline and differential.
GenevestigatoriP41229.

Interactioni

Subunit structurei

Part of two distinct complexes, one containing E2F6, and the other containing REST.1 Publication

Protein-protein interaction databases

BioGridi113870. 26 interactions.
DIPiDIP-39663N.
IntActiP41229. 3 interactions.
STRINGi9606.ENSP00000364550.

Structurei

Secondary structure

1
1560
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi73 – 764
Turni79 – 813
Helixi82 – 9413
Turni95 – 973
Helixi112 – 12211
Helixi125 – 1306
Turni131 – 1333
Helixi134 – 1407
Helixi149 – 15911
Helixi162 – 17211
Turni178 – 1803
Helixi181 – 1855

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JRZNMR-A73-188[»]
ProteinModelPortaliP41229.
SMRiP41229. Positions 13-188, 261-616.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP41229.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 5542JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini79 – 16991ARIDPROSITE-ProRule annotationAdd
BLAST
Domaini468 – 634167JmjCPROSITE-ProRule annotationAdd
BLAST

Domaini

The first PHD-type zinc finger domain recognizes and binds H3-K9Me3.
Both the JmjC domain and the JmjN domain are required for enzymatic activity.

Sequence similaritiesi

Belongs to the JARID1 histone demethylase family.Curated
Contains 1 ARID domain.PROSITE-ProRule annotation
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri326 – 37247PHD-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1187 – 124862PHD-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG327026.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiP41229.
KOiK11446.
OMAiTTSICVC.
PhylomeDBiP41229.
TreeFamiTF106476.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 2 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]
SMARTiSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: P41229-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA
60 70 80 90 100
DWQPPFAVEV DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL
110 120 130 140 150
KIPNVERRIL DLYSLSKIVV EEGGYEAICK DRRWARVAQR LNYPPGKNIG
160 170 180 190 200
SLLRSHYERI VYPYEMYQSG ANLVQCNTRP FDNEEKDKEY KPHSIPLRQS
210 220 230 240 250
VQPSKFNSYG RRAKRLQPDP EPTEEDIEKN PELKKLQIYG AGPKMMGLGL
260 270 280 290 300
MAKDKTLRKK DKEGPECPPT VVVKEELGGD VKVESTSPKT FLESKEELSH
310 320 330 340 350
SPEPCTKMTM RLRRNHSNAQ FIESYVCRMC SRGDEDDKLL LCDGCDDNYH
360 370 380 390 400
IFCLLPPLPE IPKGVWRCPK CVMAECKRPP EAFGFEQATR EYTLQSFGEM
410 420 430 440 450
ADSFKADYFN MPVHMVPTEL VEKEFWRLVN SIEEDVTVEY GADIHSKEFG
460 470 480 490 500
SGFPVSDSKR HLTPEEEEYA TSGWNLNVMP VLEQSVLCHI NADISGMKVP
510 520 530 540 550
WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL AAEHLEEVMK
560 570 580 590 600
KLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA
610 620 630 640 650
YHSGFNQGYN FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK
660 670 680 690 700
MAACPEKLDL NLAAAVHKEM FIMVQEERRL RKALLEKGIT EAEREAFELL
710 720 730 740 750
PDDERQCIKC KTTCFLSALA CYDCPDGLVC LSHINDLCKC SSSRQYLRYR
760 770 780 790 800
YTLDELPAML HKLKVRAESF DTWANKVRVA LEVEDGRKRS LEELRALESE
810 820 830 840 850
ARERRFPNSE LLQQLKNCLS EAEACVSRAL GLVSGQEAGP HRVAGLQMTL
860 870 880 890 900
TELRAFLDQM NNLPCAMHQI GDVKGVLEQV EAYQAEAREA LASLPSSPGL
910 920 930 940 950
LQSLLERGRQ LGVEVPEAQQ LQRQVEQARW LDEVKRTLAP SARRGTLAVM
960 970 980 990 1000
RGLLVAGASV APSPAVDKAQ AELQELLTIA ERWEEKAHLC LEARQKHPPA
1010 1020 1030 1040 1050
TLEAIIREAE NIPVHLPNIQ ALKEALAKAR AWIADVDEIQ NGDHYPCLDD
1060 1070 1080 1090 1100
LEGLVAVGRD LPVGLEELRQ LELQVLTAHS WREKASKTFL KKNSCYTLLE
1110 1120 1130 1140 1150
VLCPCADAGS DSTKRSRWME KELGLYKSDT ELLGLSAQDL RDPGSVIVAF
1160 1170 1180 1190 1200
KEGEQKEKEG ILQLRRTNSA KPSPLASSST ASSTTSICVC GQVLAGAGAL
1210 1220 1230 1240 1250
QCDLCQDWFH GRCVSVPRLL SSPRPNPTSS PLLAWWEWDT KFLCPLCMRS
1260 1270 1280 1290 1300
RRPRLETILA LLVALQRLPV RLPEGEALQC LTERAISWQG RARQALASED
1310 1320 1330 1340 1350
VTALLGRLAE LRQRLQAEPR PEEPPNYPAA PASDPLREGS GKDMPKVQGL
1360 1370 1380 1390 1400
LENGDSVTSP EKVAPEEGSG KRDLELLSSL LPQLTGPVLE LPEATRAPLE
1410 1420 1430 1440 1450
ELMMEGDLLE VTLDENHSIW QLLQAGQPPD LERIRTLLEL EKAERHGSRA
1460 1470 1480 1490 1500
RGRALERRRR RKVDRGGEGD DPAREELEPK RVRSSGPEAE EVQEEEELEE
1510 1520 1530 1540 1550
ETGGEGPPAP IPTTGSPSTQ ENQNGLEPAE GTTSGPSAPF STLTPRLHLP
1560
CPQQPPQQQL
Length:1,560
Mass (Da):175,720
Last modified:November 14, 2006 - v2
Checksum:i5DC673D0091E7C87
GO
Isoform 2 (identifier: P41229-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1370-1372: Missing.

Show »
Length:1,557
Mass (Da):175,379
Checksum:iB1823D7AD5F78374
GO
Isoform 3 (identifier: P41229-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     77-117: Missing.
     1370-1372: Missing.

Show »
Length:1,516
Mass (Da):170,561
Checksum:iF82BDA8A82C57C01
GO
Isoform 4 (identifier: P41229-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     51-76: Missing.
     77-117: Missing.
     1370-1372: Missing.
     1420-1560: WQLLQAGQPP...CPQQPPQQQL → PESLDFCILTPRYCSDLSSWGPAPGVFPPW

Note: No experimental confirmation available.

Show »
Length:1,379
Mass (Da):155,119
Checksum:i20A82456B8CF788E
GO
Isoform 5 (identifier: P41229-5) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     175-175: Missing.

Note: No experimental confirmation available.

Show »
Length:1,559
Mass (Da):175,592
Checksum:iCC245E4B78A1F039
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti16 – 161V → L in BAG65494. (PubMed:14702039)Curated
Sequence conflicti23 – 231E → G in BAG65494. (PubMed:14702039)Curated
Sequence conflicti342 – 3421C → Y in CAA82758. (PubMed:7951230)Curated
Sequence conflicti1199 – 11991A → R in AAA61302. (PubMed:8162017)Curated
Sequence conflicti1419 – 14191I → T in BAG65494. (PubMed:14702039)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti87 – 871D → G in MRXSCJ; no effect on subcellular location and enzymatic activity. 1 Publication
VAR_032986
Natural varianti388 – 3881A → P in MRXSCJ; impairs enzymatic activity and binding to H3-K9Me3. 1 Publication
VAR_022730
Natural varianti402 – 4021D → Y in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_022731
Natural varianti451 – 4511S → R in MRXSCJ. 1 Publication
VAR_032987
Natural varianti640 – 6401C → Y De novo mutation found in a patient with mental retardation. 1 Publication
VAR_065091
Natural varianti642 – 6421F → L in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_032988
Natural varianti698 – 6981E → K in MRXSCJ; abolishes function in vivo, but no effect on enzymatic activity or binding to H3-K9Me3. 1 Publication
VAR_022732
Natural varianti731 – 7311L → F in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_022733
Natural varianti750 – 7501R → W in MRXSCJ. 1 Publication
VAR_032989
Natural varianti751 – 7511Y → C in MRXSCJ; impairs enzymatic activity. 1 Publication
VAR_032990

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei51 – 7626Missing in isoform 4. 1 PublicationVSP_043752Add
BLAST
Alternative sequencei77 – 11741Missing in isoform 3 and isoform 4. 1 PublicationVSP_026410Add
BLAST
Alternative sequencei175 – 1751Missing in isoform 5. 1 PublicationVSP_053420
Alternative sequencei1370 – 13723Missing in isoform 2, isoform 3 and isoform 4. 1 PublicationVSP_000315
Alternative sequencei1420 – 1560141WQLLQ…PQQQL → PESLDFCILTPRYCSDLSSW GPAPGVFPPW in isoform 4. 1 PublicationVSP_043753Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L25270 mRNA. Translation: AAA61302.1.
AK304732 mRNA. Translation: BAG65494.1.
AL139396 Genomic DNA. Translation: CAI39836.1.
AL139396 Genomic DNA. Translation: CAI39837.1.
AL139396 Genomic DNA. Translation: CAI39838.1.
CH471154 Genomic DNA. Translation: EAW93145.1.
BC054499 mRNA. Translation: AAH54499.1.
Z29650 mRNA. Translation: CAA82758.1.
CCDSiCCDS14351.1. [P41229-1]
CCDS55417.1. [P41229-4]
CCDS65269.1. [P41229-5]
PIRiI54361.
RefSeqiNP_001140174.1. NM_001146702.1. [P41229-4]
NP_001269551.1. NM_001282622.1. [P41229-5]
NP_004178.2. NM_004187.3. [P41229-1]
XP_005262092.1. XM_005262035.2. [P41229-2]
UniGeneiHs.631768.

Genome annotation databases

EnsembliENST00000375379; ENSP00000364528; ENSG00000126012. [P41229-2]
ENST00000375383; ENSP00000364532; ENSG00000126012. [P41229-3]
ENST00000375401; ENSP00000364550; ENSG00000126012. [P41229-1]
ENST00000404049; ENSP00000385394; ENSG00000126012. [P41229-5]
ENST00000452825; ENSP00000445176; ENSG00000126012. [P41229-4]
GeneIDi8242.
KEGGihsa:8242.
UCSCiuc004drz.3. human. [P41229-1]
uc004dsa.3. human.
uc022bxe.1. human. [P41229-4]

Polymorphism databases

DMDMi117949812.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L25270 mRNA. Translation: AAA61302.1 .
AK304732 mRNA. Translation: BAG65494.1 .
AL139396 Genomic DNA. Translation: CAI39836.1 .
AL139396 Genomic DNA. Translation: CAI39837.1 .
AL139396 Genomic DNA. Translation: CAI39838.1 .
CH471154 Genomic DNA. Translation: EAW93145.1 .
BC054499 mRNA. Translation: AAH54499.1 .
Z29650 mRNA. Translation: CAA82758.1 .
CCDSi CCDS14351.1. [P41229-1 ]
CCDS55417.1. [P41229-4 ]
CCDS65269.1. [P41229-5 ]
PIRi I54361.
RefSeqi NP_001140174.1. NM_001146702.1. [P41229-4 ]
NP_001269551.1. NM_001282622.1. [P41229-5 ]
NP_004178.2. NM_004187.3. [P41229-1 ]
XP_005262092.1. XM_005262035.2. [P41229-2 ]
UniGenei Hs.631768.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2JRZ NMR - A 73-188 [» ]
ProteinModelPortali P41229.
SMRi P41229. Positions 13-188, 261-616.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 113870. 26 interactions.
DIPi DIP-39663N.
IntActi P41229. 3 interactions.
STRINGi 9606.ENSP00000364550.

Chemistry

ChEMBLi CHEMBL2163176.
GuidetoPHARMACOLOGYi 2682.

PTM databases

PhosphoSitei P41229.

Polymorphism databases

DMDMi 117949812.

Proteomic databases

MaxQBi P41229.
PaxDbi P41229.
PRIDEi P41229.

Protocols and materials databases

DNASUi 8242.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000375379 ; ENSP00000364528 ; ENSG00000126012 . [P41229-2 ]
ENST00000375383 ; ENSP00000364532 ; ENSG00000126012 . [P41229-3 ]
ENST00000375401 ; ENSP00000364550 ; ENSG00000126012 . [P41229-1 ]
ENST00000404049 ; ENSP00000385394 ; ENSG00000126012 . [P41229-5 ]
ENST00000452825 ; ENSP00000445176 ; ENSG00000126012 . [P41229-4 ]
GeneIDi 8242.
KEGGi hsa:8242.
UCSCi uc004drz.3. human. [P41229-1 ]
uc004dsa.3. human.
uc022bxe.1. human. [P41229-4 ]

Organism-specific databases

CTDi 8242.
GeneCardsi GC0XM053220.
HGNCi HGNC:11114. KDM5C.
MIMi 300534. phenotype.
314690. gene.
neXtProti NX_P41229.
Orphaneti 85279. Syndromic X-linked intellectual disability due to JARID1C mutation.
PharmGKBi PA35964.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG327026.
GeneTreei ENSGT00530000063118.
HOGENOMi HOG000290719.
InParanoidi P41229.
KOi K11446.
OMAi TTSICVC.
PhylomeDBi P41229.
TreeFami TF106476.

Miscellaneous databases

ChiTaRSi KDM5C. human.
EvolutionaryTracei P41229.
GeneWikii JARID1C.
GenomeRNAii 8242.
NextBioi 31002.
PROi P41229.
SOURCEi Search...

Gene expression databases

Bgeei P41229.
CleanExi HS_JARID1C.
ExpressionAtlasi P41229. baseline and differential.
Genevestigatori P41229.

Family and domain databases

Gene3Di 1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProi IPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view ]
Pfami PF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 2 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view ]
SMARTi SM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view ]
SUPFAMi SSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEi PS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and characterization of XE169, a novel human gene that escapes X-inactivation."
    Wu J., Ellison J., Salido E., Yen P., Mohandas T., Shapiro L.J.
    Hum. Mol. Genet. 3:153-160(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Fibroblast.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
    Tissue: Uterus.
  3. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5).
    Tissue: Eye.
  6. "A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human."
    Agulnik A.I., Mitchell M.J., Mattei M.-G., Borsani G., Avner P.A., Lerner J.L., Bishop C.E.
    Hum. Mol. Genet. 3:879-884(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 280-344.
    Tissue: Blood.
  7. "A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
    Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
    Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  8. "RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3."
    Christensen J., Agger K., Cloos P.A.C., Pasini D., Rose S., Sennels L., Rappsilber J., Hansen K.H., Salcini A.E., Helin K.
    Cell 128:1063-1076(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases."
    Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y.
    Cell 128:1077-1088(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR, MUTAGENESIS OF HIS-514, CHARACTERIZATION OF VARIANTS MRXSCJ PRO-388; LEU-642; PHE-731 AND CYS-751.
  10. "The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation."
    Tahiliani M., Mei P., Fang R., Leonor T., Rutenberg M., Shimizu F., Li J., Rao A., Shi Y.
    Nature 447:601-605(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, MUTAGENESIS OF HIS-514, SUBCELLULAR LOCATION, CHARACTERIZATION OF VARIANTS MRXSCJ GLY-87; TYR-402; LYS-698 AND CYS-751.
  11. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-317, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  12. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  13. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  14. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1359, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation."
    Jensen L.R., Amende M., Gurok U., Moser B., Gimmel V., Tzschach A., Janecke A.R., Tariverdian G., Chelly J., Fryns J.-P., Van Esch H., Kleefstra T., Hamel B.C.J., Moraine C., Gecz J., Turner G., Reinhardt R., Kalscheuer V.M., Ropers H.-H., Lenzner S.
    Am. J. Hum. Genet. 76:227-236(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS MRXSCJ PRO-388; TYR-402; LYS-698 AND PHE-731, TISSUE SPECIFICITY.
  17. "A novel mutation in JARID1C gene associated with mental retardation."
    Santos C., Rodriguez-Revenga L., Madrigal I., Badenas C., Pineda M., Mila M.
    Eur. J. Hum. Genet. 14:583-586(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT MRXSCJ ARG-451.
  18. Cited for: VARIANTS MRXSCJ GLY-87; LEU-642; TRP-750 AND CYS-751.
  19. Cited for: VARIANT TYR-640.

Entry informationi

Entry nameiKDM5C_HUMAN
AccessioniPrimary (citable) accession number: P41229
Secondary accession number(s): B0QZ44
, B4E3I2, F5H3T1, Q5JUX3, Q5JUX4, Q5JUX5, Q7Z5S5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 14, 2006
Last modified: October 29, 2014
This is version 150 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Escapes X-inactivation.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3