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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)DescriptionActionsGraphical viewLength
Metal bindingi514Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi517Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi602Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri326 – 372PHD-type 1PROSITE-ProRule annotationAdd BLAST47
Zinc fingeri1187 – 1248PHD-type 2PROSITE-ProRule annotationAdd BLAST62

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

BioCyciZFISH:ENSG00000126012-MONOMER.
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)DescriptionActionsGraphical viewLength
Natural variantiVAR_03298687D → G in MRXSCJ; no effect on subcellular location and enzymatic activity. 2 Publications1
Natural variantiVAR_022730388A → P in MRXSCJ; impairs enzymatic activity and binding to H3-K9Me3. 2 PublicationsCorresponds to variant rs199422235dbSNPEnsembl.1
Natural variantiVAR_022731402D → Y in MRXSCJ; decreases enzymatic activity. 3 Publications1
Natural variantiVAR_032987451S → R in MRXSCJ. 1 PublicationCorresponds to variant rs199422237dbSNPEnsembl.1
Natural variantiVAR_074308480P → L in MRXSCJ; patient fibroblasts show decreased enzymatic activity. 2 Publications1
Natural variantiVAR_032988642F → L in MRXSCJ; impairs enzymatic activity. 2 Publications1
Natural variantiVAR_022732698E → K in MRXSCJ. 1 Publication1
Natural variantiVAR_022733731L → F in MRXSCJ; impairs enzymatic activity. 2 PublicationsCorresponds to variant rs199422234dbSNPEnsembl.1
Natural variantiVAR_032989750R → W in MRXSCJ. 1 Publication1
Natural variantiVAR_032990751Y → C in MRXSCJ; impairs enzymatic activity. 3 Publications1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi514H → A: Abolishes enzymatic activity. 2 Publications1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi8242.
MalaCardsiKDM5C.
MIMi300534. phenotype.
OpenTargetsiENSG00000126012.
Orphaneti85279. Syndromic X-linked intellectual disability due to JARID1C mutation.
PharmGKBiPA35964.

Chemistry databases

ChEMBLiCHEMBL2163176.
GuidetoPHARMACOLOGYi2682.

Polymorphism and mutation databases

BioMutaiKDM5C.
DMDMi117949812.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002005861 – 1560Lysine-specific demethylase 5CAdd BLAST1560

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei287PhosphoserineCombined sources1
Modified residuei301PhosphoserineCombined sources1
Modified residuei317PhosphoserineCombined sources1
Modified residuei893PhosphoserineBy similarity1
Modified residuei897PhosphoserineCombined sources1
Modified residuei1359PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP41229.
MaxQBiP41229.
PaxDbiP41229.
PeptideAtlasiP41229.
PRIDEiP41229.

PTM databases

iPTMnetiP41229.
PhosphoSitePlusiP41229.

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 interactors.
DIPiDIP-39663N.
IntActiP41229. 21 interactors.
STRINGi9606.ENSP00000364550.

Chemistry databases

BindingDBiP41229.

Structurei

Secondary structure

11560
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi21 – 24Combined sources4
Helixi27 – 38Combined sources12
Turni39 – 41Combined sources3
Beta strandi42 – 46Combined sources5
Helixi60 – 62Combined sources3
Beta strandi68 – 71Combined sources4
Helixi73 – 76Combined sources4
Turni79 – 81Combined sources3
Helixi82 – 94Combined sources13
Turni95 – 97Combined sources3
Helixi112 – 122Combined sources11
Helixi125 – 130Combined sources6
Turni131 – 133Combined sources3
Helixi134 – 140Combined sources7
Helixi149 – 159Combined sources11
Helixi162 – 172Combined sources11
Turni178 – 180Combined sources3
Helixi181 – 185Combined sources5
Helixi394 – 409Combined sources16
Helixi418 – 429Combined sources12
Beta strandi437 – 445Combined sources9
Helixi446 – 449Combined sources4
Helixi464 – 471Combined sources8
Turni476 – 478Combined sources3
Helixi479 – 481Combined sources3
Helixi486 – 489Combined sources4
Turni495 – 497Combined sources3
Beta strandi501 – 505Combined sources5
Beta strandi510 – 514Combined sources5
Helixi517 – 519Combined sources3
Beta strandi521 – 530Combined sources10
Beta strandi532 – 536Combined sources5
Helixi539 – 541Combined sources3
Helixi542 – 552Combined sources11
Helixi573 – 577Combined sources5
Turni578 – 580Combined sources3
Beta strandi584 – 588Combined sources5
Beta strandi593 – 596Combined sources4
Beta strandi602 – 617Combined sources16
Helixi620 – 622Combined sources3
Helixi623 – 636Combined sources14
Helixi644 – 652Combined sources9
Helixi655 – 657Combined sources3
Helixi660 – 687Combined sources28
Beta strandi692 – 694Combined sources3
Helixi697 – 699Combined sources3
Helixi702 – 704Combined sources3
Turni708 – 710Combined sources3
Beta strandi716 – 723Combined sources8
Helixi731 – 733Combined sources3
Helixi742 – 744Combined sources3
Beta strandi745 – 751Combined sources7
Helixi755 – 767Combined sources13

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP41229.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini14 – 55JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini79 – 169ARIDPROSITE-ProRule annotationAdd BLAST91
Domaini468 – 634JmjCPROSITE-ProRule annotationAdd BLAST167

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)DescriptionActionsGraphical viewLength
Zinc fingeri326 – 372PHD-type 1PROSITE-ProRule annotationAdd BLAST47
Zinc fingeri1187 – 1248PHD-type 2PROSITE-ProRule annotationAdd BLAST62

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)DescriptionActionsGraphical viewLength
Sequence conflicti16V → L in BAG65494 (PubMed:14702039).Curated1
Sequence conflicti23E → G in BAG65494 (PubMed:14702039).Curated1
Sequence conflicti342C → Y in CAA82758 (PubMed:7951230).Curated1
Sequence conflicti1199A → R in AAA61302 (PubMed:8162017).Curated1
Sequence conflicti1419I → T in BAG65494 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03298687D → G in MRXSCJ; no effect on subcellular location and enzymatic activity. 2 Publications1
Natural variantiVAR_022730388A → P in MRXSCJ; impairs enzymatic activity and binding to H3-K9Me3. 2 PublicationsCorresponds to variant rs199422235dbSNPEnsembl.1
Natural variantiVAR_022731402D → Y in MRXSCJ; decreases enzymatic activity. 3 Publications1
Natural variantiVAR_032987451S → R in MRXSCJ. 1 PublicationCorresponds to variant rs199422237dbSNPEnsembl.1
Natural variantiVAR_074308480P → L in MRXSCJ; patient fibroblasts show decreased enzymatic activity. 2 Publications1
Natural variantiVAR_065091640C → Y De novo mutation found in a patient with mental retardation. 1 Publication1
Natural variantiVAR_032988642F → L in MRXSCJ; impairs enzymatic activity. 2 Publications1
Natural variantiVAR_022732698E → K in MRXSCJ. 1 Publication1
Natural variantiVAR_022733731L → F in MRXSCJ; impairs enzymatic activity. 2 PublicationsCorresponds to variant rs199422234dbSNPEnsembl.1
Natural variantiVAR_032989750R → W in MRXSCJ. 1 Publication1
Natural variantiVAR_032990751Y → C in MRXSCJ; impairs enzymatic activity. 3 Publications1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_04375251 – 76Missing in isoform 4. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_02641077 – 117Missing in isoform 3 and isoform 4. 1 PublicationAdd BLAST41
Alternative sequenceiVSP_053420175Missing in isoform 5. 1 Publication1
Alternative sequenceiVSP_0003151370 – 1372Missing in isoform 2, isoform 3 and isoform 4. 1 Publication3
Alternative sequenceiVSP_0437531420 – 1560WQLLQ…PQQQL → PESLDFCILTPRYCSDLSSW GPAPGVFPPW in isoform 4. 1 PublicationAdd BLAST141

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JRZNMR-A73-188[»]
5FWJX-ray2.10A/B8-83[»]
A/B384-772[»]
ProteinModelPortaliP41229.
SMRiP41229.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry databases

BindingDBiP41229.
ChEMBLiCHEMBL2163176.
GuidetoPHARMACOLOGYi2682.

PTM databases

iPTMnetiP41229.
PhosphoSitePlusiP41229.

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.
DisGeNETi8242.
GeneCardsiKDM5C.
HGNCiHGNC:11114. KDM5C.
MalaCardsiKDM5C.
MIMi300534. phenotype.
314690. gene.
neXtProtiNX_P41229.
OpenTargetsiENSG00000126012.
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

BioCyciZFISH:ENSG00000126012-MONOMER.
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: November 2, 2016
This is version 171 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.