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P41230 (KDM5C_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Kdm5c
Synonyms:Jarid1c, Kiaa0234, Smcx, Xe169
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1554 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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 By similarity. Ref.8

Cofactor

Alpha-ketoglutarate By similarity.

Binds 1 Fe2+ ion per subunit By similarity.

Subunit structure

Part of two distinct complexes, one containing E2F6, and the other containing REST By similarity.

Subcellular location

Nucleus By similarity.

Domain

The first PHD-type zinc finger domain recognizes and binds H3-K9Me3 By similarity.

Both the JmjC domain and the JmjN domain are required for enzymatic activity By similarity.

Miscellaneous

Escapes X-inactivation.

Sequence similarities

Belongs to the JARID1 histone demethylase family.

Contains 1 ARID domain.

Contains 1 JmjC domain.

Contains 1 JmjN domain.

Contains 2 PHD-type zinc fingers.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P41230-1)

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.
Isoform 2 (identifier: P41230-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1364-1366: Missing.
Isoform 3 (identifier: P41230-3)

The sequence of this isoform differs from the canonical sequence as follows:
     77-117: Missing.
     1364-1366: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 15541554Lysine-specific demethylase 5C
PRO_0000200587

Regions

Domain14 – 5542JmjN
Domain79 – 16991ARID
Domain468 – 634167JmjC
Zinc finger326 – 37247PHD-type 1
Zinc finger1187 – 124862PHD-type 2

Sites

Metal binding5141Iron; catalytic By similarity
Metal binding5171Iron; catalytic By similarity
Metal binding6021Iron; catalytic By similarity

Amino acid modifications

Modified residue3171Phosphoserine By similarity
Modified residue13531Phosphoserine By similarity

Natural variations

Alternative sequence77 – 11741Missing in isoform 3.
VSP_026411
Alternative sequence1364 – 13663Missing in isoform 2 and isoform 3.
VSP_000316

Experimental info

Sequence conflict31L → M in AAB96762. Ref.7
Sequence conflict261D → G in AAB96762. Ref.7
Sequence conflict1231G → S in BAE33161. Ref.2
Sequence conflict1231G → S in BAE33260. Ref.2
Sequence conflict2491G → D in BAE34464. Ref.2
Sequence conflict7261D → N in BAC97906. Ref.5
Sequence conflict8651C → L in AAD53049. Ref.1
Sequence conflict8651C → L in CAA82759. Ref.4
Sequence conflict10681L → P in CAA82759. Ref.4
Sequence conflict11261Y → C in BAE33367. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 26, 2007. Version 4.
Checksum: 585EA9F890B0D9A0

FASTA1,554175,313
        10         20         30         40         50         60 
MELGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 

        70         80         90        100        110        120 
DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERRIL DLYSLSKIVV 

       130        140        150        160        170        180 
EEGGYETICK DRRWARVAQR LNYPPGKNIG SLLRSHYERI VYPYEMYQSG ANLVQCNTRP 

       190        200        210        220        230        240 
FDNEEKDKEY KPHSIPLRQS VQPSKFNSYG RRAKRLQPDP EPTEEDIEKN PELKKLQIYG 

       250        260        270        280        290        300 
AGPKMMGLGL MAKDKTLRKK DKEGPECPPT VVVKEELGGD VKMESTSPKT FLEGKEELSH 

       310        320        330        340        350        360 
SPEPCTKMTM RLRRNHSNAQ FIESYVCRMC SRGDEDDKLL LCDGCDDNYH IFCLLPPLPE 

       370        380        390        400        410        420 
IPKGVWRCPK CVMAECKRPP EAFGFEQATR EYTLQSFGEM ADSFKADYFN MPVHMVPTEL 

       430        440        450        460        470        480 
VEKEFWRLVN SIEEDVTVEY GADIHSKEFG SGFPVSDSKR HLTPEEEEYA TSGWNLNVMP 

       490        500        510        520        530        540 
VLEQSVLCHI NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL 

       550        560        570        580        590        600 
AAEHLEEVMK KLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA 

       610        620        630        640        650        660 
YHSGFNQGYN FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAACPEKLDL 

       670        680        690        700        710        720 
NLAAAVHKEM FIMVQEERRL RKALLEKGIT EAEREAFELL PDDERQCIKC KTTCFLSALA 

       730        740        750        760        770        780 
CYDCPDGLVC LSHINDLCKC SSSRQYLRYR YTLDELPAML HKLKVRAESF DTWANKVRVA 

       790        800        810        820        830        840 
LEVEDGRKRS LEELRALESE ARERRFPNSE LLQRLKNCLS EAEACVSRAL GLVSGQEAGP 

       850        860        870        880        890        900 
DRVAGLQMTL AELRDFLGQM NNLPCAMHQI GDVKGILEQV EAYQTEAREA LVSQPSSPGL 

       910        920        930        940        950        960 
LQSLLERGQQ LGVEVPEAQQ LQRQVEQARW LDEVKRTLAP SARRGTLAIM RGLLVAGASV 

       970        980        990       1000       1010       1020 
APSPAVDKAQ AELQELLTIA ERWEEKAHLC LEARQKHPPA TLEAIIHEAE NIPVHLPNIQ 

      1030       1040       1050       1060       1070       1080 
SLKEALAKAR AWIADVDEIQ NGDHYPCLDD LEGLVAVGRD LPVGLEELRQ LELQVLTAHS 

      1090       1100       1110       1120       1130       1140 
WREKASKTFL KKNSCYTLLE VLCPCADAGS DSTKRSRWME KELGLYKSDT ELLGLSAQDL 

      1150       1160       1170       1180       1190       1200 
RDPGSVIVAF KEGEQKEKEG ILQLRRTNSA KPSPLALLTT ASSTASICVC GQVPAGVGAL 

      1210       1220       1230       1240       1250       1260 
QCDLCQDWFH GRCVTVPRLL SSQRSSLPSS PLLAWWEWDT KFLCPLCMRS RRPRLETILA 

      1270       1280       1290       1300       1310       1320 
LLVALQRLPV RLPEGEALQC LTERAISWQG RARQVLASEE VTALLGRLAE LRQRLQAESK 

      1330       1340       1350       1360       1370       1380 
PEESLAYPSD GGEGTGNMPK VQGLLENGDS VTSPEKVATE EGSGKRDLEL LSSILPQLSG 

      1390       1400       1410       1420       1430       1440 
PVLELPEATR APLEELMMEG DLLEVTLDEN HSIWQLLQAG QPPDLKRVQT LLELEKAERH 

      1450       1460       1470       1480       1490       1500 
GSRTRGRALE RRRRRKVDRG GEPDDPAREE LEPKRVRSSG PEAEEVQEEE ELEEETGGEV 

      1510       1520       1530       1540       1550 
PPVPFPNSGS PSIQEDQDGL EPVLEAGSDT SAPFSTLTSR LLMSCPQQPS LQQL 

« Hide

Isoform 2 [UniParc].

Checksum: C2061676EA2DC238
Show »

FASTA1,551174,972
Isoform 3 [UniParc].

Checksum: BAA3698F0A0A1E24
Show »

FASTA1,510170,154

References

« Hide 'large scale' references
[1]"Mouse H-Y encoding Smcy gene and its X chromosomal homolog Smcx."
Agulnik A.I., Longepied G., Ty M.T., Bishop C.E., Mitchell M.J.
Mamm. Genome 10:926-929(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
Strain: 129/SvJ.
[2]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Strain: C57BL/6J and NOD.
Tissue: Dendritic cell, Embryo, Inner ear and Small intestine.
[3]"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 3).
Strain: C57BL/6.
Tissue: Brain.
[4]"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 36-1068.
Strain: BALB/c.
Tissue: Testis.
[5]"Prediction of the coding sequences of mouse homologues of KIAA gene: III. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Nagase T., Ohara O., Koga H.
DNA Res. 10:167-180(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 165-1554 (ISOFORM 1).
Tissue: Embryonic tail.
[6]"The murine Xe169 gene escapes X-inactivation like its human homologue."
Wu J., Salido E., Yen P., Mohandas T., Shapiro L.J.
Nat. Genet. 7:491-496(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1206-1385 (ISOFORM 1).
[7]"A proposed path by which genes common to mammalian X and Y chromosomes evolve to become X inactivated."
Jegalian K.G., Page D.C.
Nature 394:776-780(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-39.
[8]"Identification of a mouse male-specific transplantation antigen, H-Y."
Scott D.M., Ehrmann I.E., Ellis P.S., Bishop C.E., Agulnik A.I., Simpson E., Mitchell M.J.
Nature 376:695-698(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
Strain: C3H.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF127245 mRNA. Translation: AAD53049.1.
AK008105 mRNA. Translation: BAB25462.1.
AK155279 mRNA. Translation: BAE33161.1.
AK155427 mRNA. Translation: BAE33260.1.
AK155651 mRNA. Translation: BAE33367.1.
AK158340 mRNA. Translation: BAE34464.1.
AK011577 mRNA. No translation available.
BC043096 mRNA. Translation: AAH43096.1.
BC054550 mRNA. Translation: AAH54550.1.
Z29651 mRNA. Translation: CAA82759.1.
AK129096 mRNA. Translation: BAC97906.1.
L29563 mRNA. Translation: AAA62384.1.
AF039894 mRNA. Translation: AAB96762.1.
CCDSCCDS41178.1. [P41230-2]
PIRI48775.
I84689.
RefSeqNP_038696.2. NM_013668.4. [P41230-2]
XP_006528832.1. XM_006528769.1. [P41230-1]
XP_006528835.1. XM_006528772.1. [P41230-3]
UniGeneMm.142655.
Mm.482277.

3D structure databases

ProteinModelPortalP41230.
SMRP41230. Positions 13-188, 261-616, 1187-1254.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid203341. 2 interactions.

PTM databases

PhosphoSiteP41230.

Proteomic databases

MaxQBP41230.
PaxDbP41230.
PRIDEP41230.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000082177; ENSMUSP00000080814; ENSMUSG00000025332. [P41230-3]
ENSMUST00000112584; ENSMUSP00000108203; ENSMUSG00000025332. [P41230-1]
ENSMUST00000112588; ENSMUSP00000108207; ENSMUSG00000025332. [P41230-2]
GeneID20591.
KEGGmmu:20591.
UCSCuc009uqc.2. mouse. [P41230-2]
uc009uqd.2. mouse. [P41230-3]
uc009uqe.2. mouse. [P41230-1]

Organism-specific databases

CTD8242.
MGIMGI:99781. Kdm5c.
RougeSearch...

Phylogenomic databases

eggNOGNOG327026.
GeneTreeENSGT00530000063118.
InParanoidP41230.
KOK11446.
OMATTSICVC.
OrthoDBEOG7D85VK.
PhylomeDBP41230.
TreeFamTF106476.

Gene expression databases

ArrayExpressP41230.
BgeeP41230.
GenevestigatorP41230.

Family and domain databases

Gene3D1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProIPR001606. 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]
PfamPF01388. 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]
SMARTSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]
SUPFAMSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEPS51011. 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]
ProtoNetSearch...

Other

ChiTaRSKDM5C. mouse.
NextBio298901.
PROP41230.
SOURCESearch...

Entry information

Entry nameKDM5C_MOUSE
AccessionPrimary (citable) accession number: P41230
Secondary accession number(s): O54995 expand/collapse secondary AC list , Q3TYU8, Q3U1X6, Q3U282, Q6ZQF8, Q80XQ9, Q9CVI4, Q9D0C3, Q9QVR8, Q9R039
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: June 26, 2007
Last modified: July 9, 2014
This is version 127 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot