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Protein

Lysine-specific demethylase 5C

Gene

KDM5C

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

Functioni

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:28262558). 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 similarity5 Publications

Miscellaneous

Escapes X-inactivation.

Cofactori

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per subunit.1 Publication

Activity regulationi

The inhibitor KDOAM-25 and others inhibit its demethylase activity, resulting to cell cycle arrest in myeloma cells.1 Publication

Kineticsi

Kcat are 1.92 min(-1) and 2.71 min(-1) for 2-oxoglutarate and histone H3K4me3, respectively.1 Publication
  1. KM=6 µM for 2-oxoglutarate1 Publication
  2. KM=3.3 µM for histone H3K4me31 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei4402-oxoglutarateBy similarity1
    Metal bindingi514Iron; catalytic1 Publication1
    Metal bindingi516Iron; catalytic1 Publication1
    Binding sitei5222-oxoglutarateBy similarity1
    Binding sitei5242-oxoglutarateBy similarity1
    Binding sitei5322-oxoglutarateBy similarity1
    Metal bindingi602Iron; catalytic1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri326 – 372PHD-type 1PROSITE-ProRule annotationAdd BLAST47
    Zinc fingeri707 – 759C5HC21 PublicationAdd BLAST53
    Zinc fingeri1187 – 1248PHD-type 2PROSITE-ProRule annotationAdd BLAST62

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase, Repressor
    Biological processBiological rhythms, Transcription, Transcription regulation
    LigandIron, 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 1C1 Publication
    Protein SmcX1 Publication
    Protein Xe169
    Gene namesi
    Name:KDM5CImported
    Synonyms:DXS1272E, JARID1C1 Publication, SMCX1 Publication, XE169
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome X

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000126012.11
    HGNCiHGNC:11114 KDM5C
    MIMi314690 gene
    neXtProtiNX_P41229

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)7 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 dbSNP:rs199422235EnsemblClinVar.1
    Natural variantiVAR_022731402D → Y in MRXSCJ; decreases enzymatic activity. 3 Publications1
    Natural variantiVAR_032987451S → R in MRXSCJ. 1 PublicationCorresponds to variant dbSNP:rs199422237EnsemblClinVar.1
    Natural variantiVAR_074308480P → L in MRXSCJ; patient fibroblasts show decreased enzymatic activity. 2 PublicationsCorresponds to variant dbSNP:rs1057518697Ensembl.1
    Natural variantiVAR_032988642F → L in MRXSCJ; impairs enzymatic activity. 2 Publications1
    Natural variantiVAR_022732698E → K in MRXSCJ. 1 PublicationCorresponds to variant dbSNP:rs1057517955Ensembl.1
    Natural variantiVAR_022733731L → F in MRXSCJ; impairs enzymatic activity. 2 PublicationsCorresponds to variant dbSNP:rs199422234EnsemblClinVar.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
    Mutagenesisi514 – 516HIE → AIA: Abolishes lysine-specific histone demethylase activity. 1 Publication3
    Mutagenesisi514H → A: Abolishes lysine-specific histone demethylase 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
    Cross-linki205Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki229Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki244Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki274Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Modified residuei287PhosphoserineCombined sources1
    Cross-linki295Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Modified residuei301PhosphoserineCombined sources1
    Modified residuei317PhosphoserineCombined sources1
    Modified residuei893PhosphoserineBy similarity1
    Modified residuei897PhosphoserineCombined sources1
    Cross-linki1127Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Modified residuei1359PhosphoserineCombined sources1

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    EPDiP41229
    MaxQBiP41229
    PaxDbiP41229
    PeptideAtlasiP41229
    PRIDEiP41229
    ProteomicsDBi55436
    55437 [P41229-2]
    55438 [P41229-3]
    55439 [P41229-4]

    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 Expressed in 221 organ(s), highest expression level in left ovary
    CleanExiHS_JARID1C
    ExpressionAtlasiP41229 baseline and differential
    GenevisibleiP41229 HS

    Organism-specific databases

    HPAiHPA038244
    HPA046147

    Interactioni

    Subunit structurei

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

    Binary interactionsi

    GO - Molecular functioni

    Protein-protein interaction databases

    BioGridi113870, 66 interactors
    DIPiDIP-39663N
    IntActiP41229, 33 interactors
    MINTiP41229
    STRINGi9606.ENSP00000364550

    Chemistry databases

    BindingDBiP41229

    Structurei

    Secondary structure

    11560
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    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

    Zinc finger

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri326 – 372PHD-type 1PROSITE-ProRule annotationAdd BLAST47
    Zinc fingeri707 – 759C5HC21 PublicationAdd BLAST53
    Zinc fingeri1187 – 1248PHD-type 2PROSITE-ProRule annotationAdd BLAST62

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiKOG1246 Eukaryota
    ENOG410XR9J LUCA
    GeneTreeiENSGT00530000063118
    HOGENOMiHOG000290719
    HOVERGENiHBG068574
    InParanoidiP41229
    KOiK11446
    OMAiCKPKHYD
    OrthoDBiEOG091G0RFR
    PhylomeDBiP41229
    TreeFamiTF106476

    Family and domain databases

    Gene3Di1.10.150.60, 1 hit
    3.30.40.10, 1 hit
    InterProiView protein in InterPro
    IPR001606 ARID_dom
    IPR036431 ARID_dom_sf
    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
    PfamiView protein in Pfam
    PF01388 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
    SMARTiView protein in SMART
    SM00501 BRIGHT, 1 hit
    SM00558 JmjC, 1 hit
    SM00545 JmjN, 1 hit
    SM00249 PHD, 2 hits
    SUPFAMiSSF46774 SSF46774, 1 hit
    SSF57903 SSF57903, 2 hits
    PROSITEiView protein in PROSITE
    PS51011 ARID, 1 hit
    PS51184 JMJC, 1 hit
    PS51183 JMJN, 1 hit
    PS01359 ZF_PHD_1, 2 hits
    PS50016 ZF_PHD_2, 1 hit

    Sequences (5+)i

    Sequence statusi: Complete.

    This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

    This entry has 5 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All

    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

    Computationally mapped potential isoform sequencesi

    There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
    EntryEntry nameProtein names
    Gene namesLengthAnnotation
    F8WF56F8WF56_HUMAN
    Lysine-specific demethylase 5C
    KDM5C
    99Annotation score:
    F8WDK1F8WDK1_HUMAN
    Lysine-specific demethylase 5C
    KDM5C
    53Annotation score:
    F8W7H7F8W7H7_HUMAN
    Lysine-specific demethylase 5C
    KDM5C
    74Annotation score:

    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 dbSNP:rs199422235EnsemblClinVar.1
    Natural variantiVAR_022731402D → Y in MRXSCJ; decreases enzymatic activity. 3 Publications1
    Natural variantiVAR_032987451S → R in MRXSCJ. 1 PublicationCorresponds to variant dbSNP:rs199422237EnsemblClinVar.1
    Natural variantiVAR_074308480P → L in MRXSCJ; patient fibroblasts show decreased enzymatic activity. 2 PublicationsCorresponds to variant dbSNP:rs1057518697Ensembl.1
    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 PublicationCorresponds to variant dbSNP:rs1057517955Ensembl.1
    Natural variantiVAR_022733731L → F in MRXSCJ; impairs enzymatic activity. 2 PublicationsCorresponds to variant dbSNP:rs199422234EnsemblClinVar.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 No translation available.
    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]
    CCDS87747.1 [P41229-2]
    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
    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

    Similar proteinsi

    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 No translation available.
    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]
    CCDS87747.1 [P41229-2]
    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
    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, 66 interactors
    DIPiDIP-39663N
    IntActiP41229, 33 interactors
    MINTiP41229
    STRINGi9606.ENSP00000364550

    Chemistry databases

    BindingDBiP41229
    ChEMBLiCHEMBL2163176
    GuidetoPHARMACOLOGYi2682

    PTM databases

    iPTMnetiP41229
    PhosphoSitePlusiP41229

    Polymorphism and mutation databases

    BioMutaiKDM5C
    DMDMi117949812

    Proteomic databases

    EPDiP41229
    MaxQBiP41229
    PaxDbiP41229
    PeptideAtlasiP41229
    PRIDEiP41229
    ProteomicsDBi55436
    55437 [P41229-2]
    55438 [P41229-3]
    55439 [P41229-4]

    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
    EuPathDBiHostDB:ENSG00000126012.11
    GeneCardsiKDM5C
    HGNCiHGNC:11114 KDM5C
    HPAiHPA038244
    HPA046147
    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
    HOVERGENiHBG068574
    InParanoidiP41229
    KOiK11446
    OMAiCKPKHYD
    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
    PROiPR:P41229
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000126012 Expressed in 221 organ(s), highest expression level in left ovary
    CleanExiHS_JARID1C
    ExpressionAtlasiP41229 baseline and differential
    GenevisibleiP41229 HS

    Family and domain databases

    Gene3Di1.10.150.60, 1 hit
    3.30.40.10, 1 hit
    InterProiView protein in InterPro
    IPR001606 ARID_dom
    IPR036431 ARID_dom_sf
    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
    PfamiView protein in Pfam
    PF01388 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
    SMARTiView protein in SMART
    SM00501 BRIGHT, 1 hit
    SM00558 JmjC, 1 hit
    SM00545 JmjN, 1 hit
    SM00249 PHD, 2 hits
    SUPFAMiSSF46774 SSF46774, 1 hit
    SSF57903 SSF57903, 2 hits
    PROSITEiView protein in PROSITE
    PS51011 ARID, 1 hit
    PS51184 JMJC, 1 hit
    PS51183 JMJN, 1 hit
    PS01359 ZF_PHD_1, 2 hits
    PS50016 ZF_PHD_2, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiKDM5C_HUMAN
    AccessioniPrimary (citable) accession number: P41229
    Secondary accession number(s): B0QZ44
    , B4E3I2, F5H3T1, Q5JUX3, Q5JUX4, Q5JUX5, Q7Z5S5
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 14, 2006
    Last modified: November 7, 2018
    This is version 188 of the entry and version 2 of the sequence. See 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

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    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. Human chromosome X
      Human chromosome X: entries, gene names and cross-references to MIM
    6. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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