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Lysine-specific demethylase 9 (KDM9) (EC 1.14.11.-) (Round spermatid basic protein 1)

 RSBN1_HUMAN             Reviewed;         802 AA.
Q5VWQ0; A8K937; Q6AI21; Q8TC33; Q9HA80; Q9NUP6;
11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
01-SEP-2009, sequence version 2.
23-MAY-2018, entry version 107.
RecName: Full=Lysine-specific demethylase 9 {ECO:0000250|UniProtKB:Q80T69};
Short=KDM9 {ECO:0000250|UniProtKB:Q80T69};
EC=1.14.11.- {ECO:0000250|UniProtKB:Q80T69};
AltName: Full=Round spermatid basic protein 1;
Name=RSBN1;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Embryo, and Placenta;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D.,
Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A.,
Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F.,
McDonald L., Evans R., Phillips K., Atkinson A., Cooper R., Jones C.,
Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P.,
Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K.,
Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G.,
Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D.,
Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G.,
Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J.,
Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R.,
Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D.,
Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G.,
Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M.,
Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J.,
Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M.,
Loveland J., Lovell J., Lush M.J., Lyne R., Martin S.,
Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S.,
Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C.,
Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z.,
Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E.,
Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A.,
Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R.,
Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V.,
Beck S., Rogers J., Bentley D.R.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 39-802 (ISOFORM 4).
TISSUE=Testis;
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).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 47-802 (ISOFORM 1).
TISSUE=Liver tumor;
PubMed=17974005; DOI=10.1186/1471-2164-8-399;
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[5]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-81, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=20068231; DOI=10.1126/scisignal.2000475;
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
Mann M.;
"Quantitative phosphoproteomics reveals widespread full
phosphorylation site occupancy during mitosis.";
Sci. Signal. 3:RA3-RA3(2010).
[6]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[7]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-781, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
Vertegaal A.C.;
"SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
Cell Rep. 10:1778-1791(2015).
[8]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-290; LYS-313; LYS-740 AND
LYS-781, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=28112733; DOI=10.1038/nsmb.3366;
Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
Nielsen M.L.;
"Site-specific mapping of the human SUMO proteome reveals co-
modification with phosphorylation.";
Nat. Struct. Mol. Biol. 24:325-336(2017).
-!- FUNCTION: Histone demethylase that specifically demethylates
dimethylated 'Lys-20' of histone H4 (H4K20me2), thereby modulating
chromosome architecture. {ECO:0000250|UniProtKB:Q80T69}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
Evidence={ECO:0000250|UniProtKB:Q80T69};
Note=Binds 1 Fe(2+) ion per subunit.
{ECO:0000250|UniProtKB:Q9GRZ3};
-!- INTERACTION:
Q8WYB5:KAT6B; NbExp=4; IntAct=EBI-1210591, EBI-948029;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q5VWQ0-1; Sequence=Displayed;
Name=4;
IsoId=Q5VWQ0-4; Sequence=VSP_027656;
-!- PTM: Phosphorylated by PKA. {ECO:0000250}.
-!- SIMILARITY: Belongs to the round spermatid basic protein 1 family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAH26155.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=BAA92075.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=BAB13974.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=CAH10493.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=CAH10493.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};
Sequence=CAH72507.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=CAI19067.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; AK002082; BAA92075.1; ALT_INIT; mRNA.
EMBL; AK292552; BAF85241.1; -; mRNA.
EMBL; AK022166; BAB13974.1; ALT_INIT; mRNA.
EMBL; AL365321; CAH72507.1; ALT_INIT; Genomic_DNA.
EMBL; AL137856; CAH72507.1; JOINED; Genomic_DNA.
EMBL; AL137856; CAI19067.1; ALT_INIT; Genomic_DNA.
EMBL; AL365321; CAI19067.1; JOINED; Genomic_DNA.
EMBL; BC026155; AAH26155.1; ALT_INIT; mRNA.
EMBL; CR627402; CAH10493.1; ALT_SEQ; mRNA.
CCDS; CCDS862.1; -. [Q5VWQ0-1]
RefSeq; NP_060834.2; NM_018364.4. [Q5VWQ0-1]
RefSeq; XP_016857007.1; XM_017001518.1. [Q5VWQ0-4]
UniGene; Hs.486285; -.
ProteinModelPortal; Q5VWQ0; -.
BioGrid; 120094; 57.
IntAct; Q5VWQ0; 6.
STRING; 9606.ENSP00000261441; -.
iPTMnet; Q5VWQ0; -.
PhosphoSitePlus; Q5VWQ0; -.
BioMuta; RSBN1; -.
DMDM; 257050986; -.
EPD; Q5VWQ0; -.
MaxQB; Q5VWQ0; -.
PaxDb; Q5VWQ0; -.
PeptideAtlas; Q5VWQ0; -.
PRIDE; Q5VWQ0; -.
DNASU; 54665; -.
Ensembl; ENST00000261441; ENSP00000261441; ENSG00000081019. [Q5VWQ0-1]
Ensembl; ENST00000612242; ENSP00000479490; ENSG00000081019. [Q5VWQ0-1]
GeneID; 54665; -.
KEGG; hsa:54665; -.
UCSC; uc001edq.4; human. [Q5VWQ0-1]
CTD; 54665; -.
DisGeNET; 54665; -.
EuPathDB; HostDB:ENSG00000081019.13; -.
GeneCards; RSBN1; -.
H-InvDB; HIX0000902; -.
HGNC; HGNC:25642; RSBN1.
HPA; HPA042124; -.
HPA; HPA049484; -.
MIM; 615858; gene.
neXtProt; NX_Q5VWQ0; -.
OpenTargets; ENSG00000081019; -.
PharmGKB; PA134869532; -.
eggNOG; KOG4425; Eukaryota.
eggNOG; ENOG410XSZP; LUCA.
GeneTree; ENSGT00390000001969; -.
HOGENOM; HOG000043117; -.
HOVERGEN; HBG094904; -.
InParanoid; Q5VWQ0; -.
OMA; GDLKHKD; -.
OrthoDB; EOG091G026S; -.
PhylomeDB; Q5VWQ0; -.
TreeFam; TF323256; -.
ChiTaRS; RSBN1; human.
GenomeRNAi; 54665; -.
PRO; PR:Q5VWQ0; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000081019; -.
CleanEx; HS_RSBN1; -.
ExpressionAtlas; Q5VWQ0; baseline and differential.
Genevisible; Q5VWQ0; HS.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
InterPro; IPR026306; RSBN1/Dpy-21.
PANTHER; PTHR13354; PTHR13354; 1.
1: Evidence at protein level;
Alternative splicing; Chromatin regulator; Complete proteome;
Dioxygenase; Iron; Isopeptide bond; Metal-binding; Nucleus;
Oxidoreductase; Phosphoprotein; Reference proteome; Ubl conjugation.
CHAIN 1 802 Lysine-specific demethylase 9.
/FTId=PRO_0000299412.
MOTIF 252 263 Nuclear localization signal.
{ECO:0000255}.
COMPBIAS 103 165 Pro-rich.
COMPBIAS 114 117 Poly-Arg.
COMPBIAS 185 197 His-rich.
COMPBIAS 252 261 Poly-Lys.
METAL 582 582 Iron, catalytic.
{ECO:0000250|UniProtKB:Q9GRZ3}.
METAL 584 584 Iron, catalytic.
{ECO:0000250|UniProtKB:Q9GRZ3}.
METAL 684 684 Iron, catalytic.
{ECO:0000250|UniProtKB:Q9GRZ3}.
BINDING 579 579 Alpha-ketoglutarate.
{ECO:0000250|UniProtKB:Q9GRZ3}.
BINDING 676 676 Alpha-ketoglutarate.
{ECO:0000250|UniProtKB:Q9GRZ3}.
MOD_RES 81 81 Phosphoserine.
{ECO:0000244|PubMed:20068231}.
CROSSLNK 290 290 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
CROSSLNK 313 313 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
CROSSLNK 740 740 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
CROSSLNK 781 781 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:25772364,
ECO:0000244|PubMed:28112733}.
VAR_SEQ 460 802 Missing (in isoform 4).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_027656.
CONFLICT 39 40 GP -> SG (in Ref. 3; AAH26155).
{ECO:0000305}.
CONFLICT 106 106 E -> G (in Ref. 1; BAF85241).
{ECO:0000305}.
CONFLICT 120 120 Q -> R (in Ref. 1; BAA92075).
{ECO:0000305}.
SEQUENCE 802 AA; 90072 MW; 78F229AB6A0FABD1 CRC64;
MFISGRRTAD KWRAEERLQC PAGSARAALA RCADGGAVGP FKCVFVGEMA AQVGAVRVVR
AVAAQEEPDK EGKEKPHAGV SPRGVKRQRR SSSGGSQEKR GRPSQEPPLA PPHRRRRSRQ
HPGPLPPTNA APTVPGPVEP LLLPPPPPPS LAPAGPAVAA PLPAPSTSAL FTFSPLTVSA
AGPKHKGHKE RHKHHHHRGP DGDPSSCGTD LKHKDKQENG ERTGGVPLIK APKRETPDEN
GKTQRADDFV LKKIKKKKKK KHREDMRGRR LKMYNKEVQT VCAGLTRISK EILTQGQINS
TSGLNKESFR YLKDEQLCRL NLGMQEYRVP QGVQTPFMTH QEHSIRRNFL KTGTKFSNFI
HEEHQSNGGA LVLHAYMDEL SFLSPMEMER FSEEFLALTF SENEKNAAYY ALAIVHGAAA
YLPDFLDYFA FNFPNTPVKM EILGKKDIET TTISNFHTQV NRTYCCGTYR AGPMRQISLV
GAVDEEVGDY FPEFLDMLEE SPFLKMTLPW GTLSSLRLQC RSQSDDGPIM WVRPGEQMIP
TADMPKSPFK RRRSMNEIKN LQYLPRTSEP REVLFEDRTR AHADHVGQGF DWQSTAAVGV
LKAVQFGEWS DQPRITKDVI CFHAEDFTDV VQRLQLDLHE PPVSQCVQWV DEAKLNQMRR
EGIRYARIQL CDNDIYFIPR NVIHQFKTVS AVCSLAWHIR LKQYHPVVEA TQNTESNSNM
DCGLTGKREL EVDSQCVRIK TESEEACTEI QLLTTASSSF PPASELNLQQ DQKTQPIPVL
KVESRLDSDQ QHNLQEHSTT SV


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