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Lysine-specific demethylase 3A (EC 1.14.11.-) (JmjC domain-containing histone demethylation protein 2A) (Jumonji domain-containing protein 1A)

 KDM3A_MOUSE             Reviewed;        1323 AA.
Q6PCM1; Q2MJQ6; Q3TKW8; Q3UML3; Q6ZQ57; Q8K2J6; Q8K2K4; Q8R350;
22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
05-JUL-2004, sequence version 1.
20-JUN-2018, entry version 122.
RecName: Full=Lysine-specific demethylase 3A;
EC=1.14.11.-;
AltName: Full=JmjC domain-containing histone demethylation protein 2A;
AltName: Full=Jumonji domain-containing protein 1A;
Name=Kdm3a; Synonyms=Jhdm2a, Jmjd1a, Kiaa0742;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Embryonic tail;
PubMed=14621295; DOI=10.1093/dnares/10.4.167;
Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
Saga Y., Nagase T., Ohara O., Koga H.;
"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.";
DNA Res. 10:167-180(2003).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND NUCLEOTIDE
SEQUENCE [LARGE SCALE MRNA] OF 1-1034 (ISOFORM 2).
STRAIN=C57BL/6J, Czech II, and FVB/N; TISSUE=Brain, and Mammary tumor;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-834.
TISSUE=Lung;
PubMed=16141072; DOI=10.1126/science.1112014;
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., 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.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[4]
NUCLEOTIDE SEQUENCE [MRNA] OF 115-1323.
STRAIN=BALB/cJ; TISSUE=Testis;
Knebel J., De Haro L., Janknecht R.;
"Characterization of murine Jmjd1a/TSGA.";
Submitted (DEC-2005) to the EMBL/GenBank/DDBJ databases.
[5]
FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL
STAGE.
PubMed=17943087; DOI=10.1038/nature06236;
Okada Y., Scott G., Ray M.K., Mishina Y., Zhang Y.;
"Histone demethylase JHDM2A is critical for Tnp1 and Prm1
transcription and spermatogenesis.";
Nature 450:119-123(2007).
[6]
FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
PubMed=19194461; DOI=10.1038/nature07777;
Tateishi K., Okada Y., Kallin E.M., Zhang Y.;
"Role of Jhdm2a in regulating metabolic gene expression and obesity
resistance.";
Nature 458:757-761(2009).
[7]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
-!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-
9' of histone H3, thereby playing a central role in histone code.
Preferentially demethylates mono- and dimethylated H3 'Lys-9'
residue, with a preference for dimethylated residue, while it has
weak or no activity on trimethylated H3 'Lys-9'. Demethylation of
Lys residue generates formaldehyde and succinate. Involved in
hormone-dependent transcriptional activation, by participating in
recruitment to androgen-receptor target genes, resulting in H3
'Lys-9' demethylation and transcriptional activation (By
similarity). Involved in spermatogenesis by regulating expression
of target genes such as PRM1 and TNP1 which are required for
packaging and condensation of sperm chromatin (PubMed:17943087).
Involved in obesity resistance through regulation of metabolic
genes such as PPARA and UCP1. {ECO:0000250,
ECO:0000269|PubMed:17943087, ECO:0000269|PubMed:19194461}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17943087}.
Nucleus {ECO:0000269|PubMed:17943087}. Note=Nuclear in round
spermatids. When spermatids start to elongate, localizes to the
cytoplasm where it forms distinct foci which disappear in mature
spermatozoa.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q6PCM1-1; Sequence=Displayed;
Name=2;
IsoId=Q6PCM1-2; Sequence=VSP_018296, VSP_018297;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Highly expressed in testis (at protein level).
Also expressed at high levels in tissues responsive to sympathetic
nerve activity such as brown adipose tissue and skeletal muscle.
{ECO:0000269|PubMed:17943087}.
-!- DEVELOPMENTAL STAGE: Expression increases significantly during
spermatogenesis with a 70-fold increase from day 7 testis to day
30 testis. First detected in the late pachytene stage, increases
in diplotene and secondary spermatocytes and reaches its highest
levels in round spermatids. {ECO:0000269|PubMed:17943087}.
-!- INDUCTION: By beta-adrenergic stimulation (at protein level).
{ECO:0000269|PubMed:19194461}.
-!- DOMAIN: The JmjC domain and the C6-type zinc-finger are required
for the demethylation activity. {ECO:0000250}.
-!- DOMAIN: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate
the association with nuclear receptors. {ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Spermatogenesis defects and adult obesity.
{ECO:0000269|PubMed:19194461}.
-!- SIMILARITY: Belongs to the JHDM2 histone demethylase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAC98014.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; AK129204; BAC98014.1; ALT_INIT; mRNA.
EMBL; BC026605; AAH26605.1; -; mRNA.
EMBL; BC031158; AAH31158.1; -; mRNA.
EMBL; BC031200; AAH31200.1; -; mRNA.
EMBL; BC059264; AAH59264.1; -; mRNA.
EMBL; AK144825; BAE26085.1; -; mRNA.
EMBL; AK166797; BAE39025.1; -; mRNA.
EMBL; DQ323991; ABC54567.1; -; mRNA.
CCDS; CCDS20233.1; -. [Q6PCM1-1]
RefSeq; NP_001033784.2; NM_001038695.3. [Q6PCM1-1]
RefSeq; NP_766589.1; NM_173001.3. [Q6PCM1-1]
RefSeq; XP_006505327.1; XM_006505264.3. [Q6PCM1-1]
UniGene; Mm.260479; -.
ProteinModelPortal; Q6PCM1; -.
SMR; Q6PCM1; -.
BioGrid; 222501; 1.
IntAct; Q6PCM1; 1.
STRING; 10090.ENSMUSP00000065716; -.
iPTMnet; Q6PCM1; -.
PhosphoSitePlus; Q6PCM1; -.
EPD; Q6PCM1; -.
PaxDb; Q6PCM1; -.
PeptideAtlas; Q6PCM1; -.
PRIDE; Q6PCM1; -.
Ensembl; ENSMUST00000065509; ENSMUSP00000065716; ENSMUSG00000053470. [Q6PCM1-1]
Ensembl; ENSMUST00000167220; ENSMUSP00000128789; ENSMUSG00000053470. [Q6PCM1-1]
Ensembl; ENSMUST00000207023; ENSMUSP00000145959; ENSMUSG00000053470. [Q6PCM1-1]
GeneID; 104263; -.
KEGG; mmu:104263; -.
UCSC; uc009cgy.3; mouse. [Q6PCM1-1]
CTD; 55818; -.
MGI; MGI:98847; Kdm3a.
eggNOG; KOG1356; Eukaryota.
eggNOG; ENOG410XTAA; LUCA.
GeneTree; ENSGT00530000063039; -.
InParanoid; Q6PCM1; -.
KO; K15601; -.
OMA; NVFRECW; -.
OrthoDB; EOG091G00RB; -.
PhylomeDB; Q6PCM1; -.
TreeFam; TF324723; -.
BRENDA; 1.14.11.B1; 3474.
Reactome; R-MMU-3214842; HDMs demethylate histones.
ChiTaRS; Kdm3a; mouse.
PRO; PR:Q6PCM1; -.
Proteomes; UP000000589; Chromosome 6.
Bgee; ENSMUSG00000053470; -.
CleanEx; MM_JMJD1A; -.
ExpressionAtlas; Q6PCM1; baseline and differential.
Genevisible; Q6PCM1; MM.
GO; GO:0000785; C:chromatin; IBA:GO_Central.
GO; GO:0005737; C:cytoplasm; IDA:MGI.
GO; GO:0005654; C:nucleoplasm; ISO:MGI.
GO; GO:0005634; C:nucleus; IDA:MGI.
GO; GO:0050681; F:androgen receptor binding; ISO:MGI.
GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
GO; GO:0003700; F:DNA binding transcription factor activity; IDA:MGI.
GO; GO:0032454; F:histone demethylase activity (H3-K9 specific); ISO:MGI.
GO; GO:0005506; F:iron ion binding; ISO:MGI.
GO; GO:0000979; F:RNA polymerase II core promoter sequence-specific DNA binding; IDA:MGI.
GO; GO:0000976; F:transcription regulatory region sequence-specific DNA binding; IDA:MGI.
GO; GO:0030521; P:androgen receptor signaling pathway; ISO:MGI.
GO; GO:1990830; P:cellular response to leukemia inhibitory factor; IEP:MGI.
GO; GO:0046293; P:formaldehyde biosynthetic process; ISO:MGI.
GO; GO:0033169; P:histone H3-K9 demethylation; IMP:MGI.
GO; GO:0036123; P:histone H3-K9 dimethylation; IDA:MGI.
GO; GO:0009755; P:hormone-mediated signaling pathway; ISO:MGI.
GO; GO:0051573; P:negative regulation of histone H3-K9 methylation; IMP:MGI.
GO; GO:0010628; P:positive regulation of gene expression; ISO:MGI.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:MGI.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISO:MGI.
GO; GO:0010468; P:regulation of gene expression; IMP:MGI.
GO; GO:2000736; P:regulation of stem cell differentiation; IMP:MGI.
GO; GO:2000036; P:regulation of stem cell population maintenance; IGI:MGI.
GO; GO:0007290; P:spermatid nucleus elongation; IMP:MGI.
GO; GO:0007283; P:spermatogenesis; IMP:MGI.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR003347; JmjC_dom.
Pfam; PF02373; JmjC; 1.
SMART; SM00558; JmjC; 1.
PROSITE; PS51184; JMJC; 1.
1: Evidence at protein level;
Acetylation; Activator; Alternative splicing; Chromatin regulator;
Complete proteome; Cytoplasm; Differentiation; Dioxygenase; Iron;
Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein;
Reference proteome; Spermatogenesis; Transcription;
Transcription regulation; Zinc; Zinc-finger.
CHAIN 1 1323 Lysine-specific demethylase 3A.
/FTId=PRO_0000084286.
DOMAIN 1060 1283 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
ZN_FING 662 687 C6-type. {ECO:0000255}.
MOTIF 885 889 LXXLL motif.
METAL 1122 1122 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 1124 1124 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 1251 1251 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
MOD_RES 264 264 Phosphoserine.
{ECO:0000250|UniProtKB:Q9Y4C1}.
MOD_RES 325 325 Phosphoserine.
{ECO:0000250|UniProtKB:Q9Y4C1}.
MOD_RES 446 446 Phosphoserine.
{ECO:0000250|UniProtKB:Q9Y4C1}.
MOD_RES 895 895 N6-acetyllysine.
{ECO:0000250|UniProtKB:Q9Y4C1}.
VAR_SEQ 1 492 Missing (in isoform 2).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_018296.
VAR_SEQ 493 507 NESCCTRSSNKTQTP -> MFWGDWKNIMEGAPA (in
isoform 2).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_018297.
CONFLICT 144 144 K -> Q (in Ref. 4; ABC54567).
{ECO:0000305}.
CONFLICT 229 229 P -> L (in Ref. 4; ABC54567).
{ECO:0000305}.
CONFLICT 618 618 A -> T (in Ref. 4; ABC54567).
{ECO:0000305}.
CONFLICT 832 832 V -> F (in Ref. 2; AAH31200).
{ECO:0000305}.
SEQUENCE 1323 AA; 147847 MW; 6D9C4A7779076AED CRC64;
MVLTLGESWP VLVGKRFLSL SAAEGNEGGQ DNWDLERVAE WPWLSGTIRA VSHTDVTKKD
LKVCVEFDGE SWRKRRWIDV YSLQRKAFLV EHNLVLAERK SPEVPEQVIQ WPAIMYKSLL
DKAGLGAITS VRFLGDQQSV FVSKDLLKPI QDVNSLRLSL TDNQTVSKEF QALIVKHLDE
SHLLQGDKNL VGSEVKIYSL DPSTQWFSAT VVHGNPSSKT LQVNCEEIPA LKIVDPALIH
VEVVHDNFVT CGNSTRTGAV KRKSSENNGS SVSKQAKSCS EASPSMCPVQ SVPTTVFKEI
LLGCTAATPS SKDPRQQNTP QAANSPPNIG AKLPQGCHKQ NLPEELSSCL NTKPEVPRTK
PDVCKEGLLS SKSSQVGAGD LKILSEPKGS CIQPKTNTDQ ESRLESAPQP VTGLPKECLP
AKTSSKAELD IATTPELQKH LEHAASTSDD LSDKPEVKAG VTSLNSCAEK KVEPSHLGSQ
SQNLKETSVK VDNESCCTRS SNKTQTPPAR KSVLTDPDKV RKLQQSGEAF VQDDSCVNIV
AQLPKCRECR LDSLRKDKDQ QKDSPVFCRF FHFRRLQFNK HGVLRVEGFL TPNKYDSEAI
GLWLPLTKNV VGTDLDTAKY ILANIGDHFC QMVISEKEAM STIEPHRQVA WKRAVKGVRE
MCDVCDTTIF NLHWVCPRCG FGVCVDCYRM KRKNCQQGAA YKTFSWIRCV KSQIHEPENL
MPTQIIPGKA LYDVGDIVHS VRAKWGIKAN CPCSNRQFKL FSKPALKEDL KQTSLSGEKP
TLGTMVQQSS PVLEPVAVCG EAASKPASSV KPTCPTSTSP LNWLADLTSG NVNKENKEKQ
LTMPILKNEI KCLPPLPPLN KPSTVLHTFN STILTPVSNN NSGFLRNLLN SSTAKTENGL
KNTPKILDDI FASLVQNKTS SDSSKRPQGL TIKPSILGFD TPHYWLCDNR LLCLQDPNNK
SNWNVFRECW KQGQPVMVSG VHHKLNTELW KPESFRKEFG EQEVDLVNCR TNEIITGATV
GDFWDGFEDV PNRLKNDKEK EPMVLKLKDW PPGEDFRDMM PSRFDDLMAN IPLPEYTRRD
GKLNLASRLP NYFVRPDLGP KMYNAYGLIT PEDRKYGTTN LHLDVSDAAN VMVYVGIPKG
QCEQEEEVLR TIQDGDSDEL TIKRFIEGKE KPGALWHIYA AKDTEKIREF LKKVSEEQGQ
DNPADHDPIH DQSWYLDRSL RKRLYQEYGV QGWAIVQFLG DVVFIPAGAP HQVHNLYSCI
KVAEDFVSPE HVKHCFWLTQ EFRYLSQTHT NHEDKLQVKN VIYHAVKDAV AMLKASESSL
GKP


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