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Protein

Lysine-specific demethylase 5C

Gene

KDM5C

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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

Protein has several cofactor binding sites:

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

GO - Biological processi

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

Enzyme and pathway databases

BRENDAi1.14.11.B2. 2681.
ReactomeiR-HSA-3214842. HDMs demethylate histones.

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
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:11114. KDM5C.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: Reactome
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)5 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:300534
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti87 – 871D → G in MRXSCJ; no effect on subcellular location and enzymatic activity. 2 Publications
VAR_032986
Natural varianti388 – 3881A → P in MRXSCJ; impairs enzymatic activity and binding to H3-K9Me3. 2 Publications
Corresponds to variant rs199422235 [ dbSNP | Ensembl ].
VAR_022730
Natural varianti402 – 4021D → Y in MRXSCJ; decreases enzymatic activity. 3 Publications
VAR_022731
Natural varianti451 – 4511S → R in MRXSCJ. 1 Publication
Corresponds to variant rs199422237 [ dbSNP | Ensembl ].
VAR_032987
Natural varianti480 – 4801P → L in MRXSCJ; patient fibroblasts show decreased enzymatic activity. 2 Publications
VAR_074308
Natural varianti642 – 6421F → L in MRXSCJ; impairs enzymatic activity. 2 Publications
VAR_032988
Natural varianti698 – 6981E → K in MRXSCJ. 1 Publication
VAR_022732
Natural varianti731 – 7311L → F in MRXSCJ; impairs enzymatic activity. 2 Publications
Corresponds to variant rs199422234 [ dbSNP | Ensembl ].
VAR_022733
Natural varianti750 – 7501R → W in MRXSCJ. 1 Publication
VAR_032989
Natural varianti751 – 7511Y → C in MRXSCJ; impairs enzymatic activity. 3 Publications
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

MalaCardsiKDM5C.
MIMi300534. phenotype.
Orphaneti85279. Syndromic X-linked intellectual disability due to JARID1C mutation.
PharmGKBiPA35964.

Chemistry

ChEMBLiCHEMBL2163176.
GuidetoPHARMACOLOGYi2682.

Polymorphism and mutation databases

BioMutaiKDM5C.
DMDMi117949812.

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 residuei287 – 2871PhosphoserineCombined sources
Modified residuei301 – 3011PhosphoserineCombined sources
Modified residuei317 – 3171PhosphoserineCombined sources
Modified residuei893 – 8931PhosphoserineBy similarity
Modified residuei897 – 8971PhosphoserineCombined sources
Modified residuei1359 – 13591PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP41229.
MaxQBiP41229.
PaxDbiP41229.
PeptideAtlasiP41229.
PRIDEiP41229.

PTM databases

iPTMnetiP41229.
PhosphoSiteiP41229.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000126012.
CleanExiHS_JARID1C.
ExpressionAtlasiP41229. baseline and differential.
GenevisibleiP41229. HS.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi113870. 51 interactions.
DIPiDIP-39663N.
IntActiP41229. 21 interactions.
STRINGi9606.ENSP00000364550.

Chemistry

BindingDBiP41229.

Structurei

Secondary structure

1
1560
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 244Combined sources
Helixi27 – 3812Combined sources
Turni39 – 413Combined sources
Beta strandi42 – 465Combined sources
Helixi60 – 623Combined sources
Beta strandi68 – 714Combined sources
Helixi73 – 764Combined sources
Turni79 – 813Combined sources
Helixi82 – 9413Combined sources
Turni95 – 973Combined sources
Helixi112 – 12211Combined sources
Helixi125 – 1306Combined sources
Turni131 – 1333Combined sources
Helixi134 – 1407Combined sources
Helixi149 – 15911Combined sources
Helixi162 – 17211Combined sources
Turni178 – 1803Combined sources
Helixi181 – 1855Combined sources
Helixi394 – 40916Combined sources
Helixi418 – 42912Combined sources
Beta strandi437 – 4459Combined sources
Helixi446 – 4494Combined sources
Helixi464 – 4718Combined sources
Turni476 – 4783Combined sources
Helixi479 – 4813Combined sources
Helixi486 – 4894Combined sources
Turni495 – 4973Combined sources
Beta strandi501 – 5055Combined sources
Beta strandi510 – 5145Combined sources
Helixi517 – 5193Combined sources
Beta strandi521 – 53010Combined sources
Beta strandi532 – 5365Combined sources
Helixi539 – 5413Combined sources
Helixi542 – 55211Combined sources
Helixi573 – 5775Combined sources
Turni578 – 5803Combined sources
Beta strandi584 – 5885Combined sources
Beta strandi593 – 5964Combined sources
Beta strandi602 – 61716Combined sources
Helixi620 – 6223Combined sources
Helixi623 – 63614Combined sources
Helixi644 – 6529Combined sources
Helixi655 – 6573Combined sources
Helixi660 – 68728Combined sources
Beta strandi692 – 6943Combined sources
Helixi697 – 6993Combined sources
Helixi702 – 7043Combined sources
Turni708 – 7103Combined sources
Beta strandi716 – 7238Combined sources
Helixi731 – 7333Combined sources
Helixi742 – 7443Combined sources
Beta strandi745 – 7517Combined sources
Helixi755 – 76713Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JRZNMR-A73-188[»]
5FWJX-ray2.10A/B8-83[»]
A/B384-772[»]
ProteinModelPortaliP41229.
SMRiP41229. Positions 8-188, 319-768.
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

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiP41229.
KOiK11446.
OMAiLQQCNTR.
OrthoDBiEOG091G0RFR.
PhylomeDBiP41229.
TreeFamiTF106476.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR001606. ARID_dom.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR013637. Lys_sp_deMease-like_dom.
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. 1 hit.
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. AlignAdd to basket

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. 2 Publications
VAR_032986
Natural varianti388 – 3881A → P in MRXSCJ; impairs enzymatic activity and binding to H3-K9Me3. 2 Publications
Corresponds to variant rs199422235 [ dbSNP | Ensembl ].
VAR_022730
Natural varianti402 – 4021D → Y in MRXSCJ; decreases enzymatic activity. 3 Publications
VAR_022731
Natural varianti451 – 4511S → R in MRXSCJ. 1 Publication
Corresponds to variant rs199422237 [ dbSNP | Ensembl ].
VAR_032987
Natural varianti480 – 4801P → L in MRXSCJ; patient fibroblasts show decreased enzymatic activity. 2 Publications
VAR_074308
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. 2 Publications
VAR_032988
Natural varianti698 – 6981E → K in MRXSCJ. 1 Publication
VAR_022732
Natural varianti731 – 7311L → F in MRXSCJ; impairs enzymatic activity. 2 Publications
Corresponds to variant rs199422234 [ dbSNP | Ensembl ].
VAR_022733
Natural varianti750 – 7501R → W in MRXSCJ. 1 Publication
VAR_032989
Natural varianti751 – 7511Y → C in MRXSCJ; impairs enzymatic activity. 3 Publications
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:
EMBLi
GenBanki
DDBJi
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_005262035.4. [P41229-2]
XP_011529128.1. XM_011530826.2. [P41229-3]
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.4. human. [P41229-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_005262035.4. [P41229-2]
XP_011529128.1. XM_011530826.2. [P41229-3]
UniGeneiHs.631768.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JRZNMR-A73-188[»]
5FWJX-ray2.10A/B8-83[»]
A/B384-772[»]
ProteinModelPortaliP41229.
SMRiP41229. Positions 8-188, 319-768.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113870. 51 interactions.
DIPiDIP-39663N.
IntActiP41229. 21 interactions.
STRINGi9606.ENSP00000364550.

Chemistry

BindingDBiP41229.
ChEMBLiCHEMBL2163176.
GuidetoPHARMACOLOGYi2682.

PTM databases

iPTMnetiP41229.
PhosphoSiteiP41229.

Polymorphism and mutation databases

BioMutaiKDM5C.
DMDMi117949812.

Proteomic databases

EPDiP41229.
MaxQBiP41229.
PaxDbiP41229.
PeptideAtlasiP41229.
PRIDEiP41229.

Protocols and materials databases

DNASUi8242.
Structural Biology KnowledgebaseSearch...

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.4. human. [P41229-1]

Organism-specific databases

CTDi8242.
GeneCardsiKDM5C.
HGNCiHGNC:11114. KDM5C.
MalaCardsiKDM5C.
MIMi300534. phenotype.
314690. gene.
neXtProtiNX_P41229.
Orphaneti85279. Syndromic X-linked intellectual disability due to JARID1C mutation.
PharmGKBiPA35964.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiP41229.
KOiK11446.
OMAiLQQCNTR.
OrthoDBiEOG091G0RFR.
PhylomeDBiP41229.
TreeFamiTF106476.

Enzyme and pathway databases

BRENDAi1.14.11.B2. 2681.
ReactomeiR-HSA-3214842. HDMs demethylate histones.

Miscellaneous databases

ChiTaRSiKDM5C. human.
EvolutionaryTraceiP41229.
GeneWikiiJARID1C.
GenomeRNAii8242.
PROiP41229.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000126012.
CleanExiHS_JARID1C.
ExpressionAtlasiP41229. baseline and differential.
GenevisibleiP41229. HS.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR001606. ARID_dom.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR013637. Lys_sp_deMease-like_dom.
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. 1 hit.
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]
ProtoNetiSearch...

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: September 7, 2016
This is version 169 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.