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Protein

RNA-binding protein 12B

Gene

RBM12B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 12B
Alternative name(s):
RNA-binding motif protein 12B
Gene namesi
Name:RBM12B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 8

Organism-specific databases

HGNCiHGNC:32310. RBM12B.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142671098.

Polymorphism and mutation databases

BioMutaiRBM12B.
DMDMi215273872.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10011001RNA-binding protein 12BPRO_0000273366Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei112 – 1121PhosphoserineCombined sources
Cross-linki151 – 151Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei250 – 2501PhosphoserineCombined sources
Modified residuei254 – 2541PhosphoserineCombined sources
Modified residuei276 – 2761PhosphothreonineCombined sources
Modified residuei278 – 2781PhosphoserineCombined sources
Modified residuei280 – 2801PhosphoserineCombined sources
Modified residuei319 – 3191N6-acetyllysineCombined sources
Modified residuei575 – 5751PhosphoserineCombined sources
Modified residuei638 – 6381PhosphoserineCombined sources
Modified residuei640 – 6401PhosphothreonineCombined sources
Modified residuei710 – 7101PhosphoserineCombined sources
Modified residuei718 – 7181PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8IXT5.
MaxQBiQ8IXT5.
PaxDbiQ8IXT5.
PRIDEiQ8IXT5.

PTM databases

iPTMnetiQ8IXT5.
PhosphoSiteiQ8IXT5.

Expressioni

Gene expression databases

BgeeiQ8IXT5.
CleanExiHS_RBM12B.
ExpressionAtlasiQ8IXT5. baseline and differential.
GenevisibleiQ8IXT5. HS.

Organism-specific databases

HPAiHPA024398.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
CACNA1AO005552EBI-3044077,EBI-766279

Protein-protein interaction databases

BioGridi133227. 20 interactions.
IntActiQ8IXT5. 16 interactions.
STRINGi9606.ENSP00000382239.

Structurei

3D structure databases

ProteinModelPortaliQ8IXT5.
SMRiQ8IXT5. Positions 146-239, 274-373, 399-486, 925-1000.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini155 – 23076RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini284 – 36077RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini400 – 47778RRM 3PROSITE-ProRule annotationAdd
BLAST
Domaini925 – 100177RRM 4PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 4 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG4307. Eukaryota.
ENOG4111WZ9. LUCA.
GeneTreeiENSGT00760000119102.
HOGENOMiHOG000231575.
HOVERGENiHBG057691.
InParanoidiQ8IXT5.
OMAiEHFRRPP.
OrthoDBiEOG77DJ57.
PhylomeDBiQ8IXT5.
TreeFamiTF331899.

Family and domain databases

Gene3Di3.30.70.330. 5 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 5 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 5 hits.
PROSITEiPS50102. RRM. 4 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8IXT5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVVIRLLGL PFIAGPVDIR HFFTGLTIPD GGVHIIGGEI GEAFIIFATD
60 70 80 90 100
EDARRAISRS GGFIKDSSVE LFLSSKAEMQ KTIEMKRTDR VGRGRPGSGT
110 120 130 140 150
SGVDSLSNFI ESVKEEASNS GYGSSINQDA GFHTNGTGHG NLRPRKTRPL
160 170 180 190 200
KAENPYLFLR GLPYLVNEDD VRVFFSGLCV DGVIFLKHHD GRNNGDAIVK
210 220 230 240 250
FASCVDASGG LKCHRSFMGS RFIEVMQGSE QQWIEFGGNA VKEGDVLRRS
260 270 280 290 300
EEHSPPRGIN DRHFRKRSHS KSPRRTRSRS PLGFYVHLKN LSLSIDERDL
310 320 330 340 350
RNFFRGTDLT DEQIRFLYKD ENRTRYAFVM FKTLKDYNTA LSLHKTVLQY
360 370 380 390 400
RPVHIDPISR KQMLKFIARY EKKRSGSLER DRPGHVSQKY SQEGNSGQKL
410 420 430 440 450
CIYIRNFPFD VTKVEVQKFF ADFLLAEDDI YLLYDDKGVG LGEALVKFKS
460 470 480 490 500
EEQAMKAERL NRRRFLGTEV LLRLISEAQI QEFGVNFSVM SSEKMQARSQ
510 520 530 540 550
SRERGDHSHL FDSKDPPIYS VGAFENFRHQ LEDLRQLDNF KHPQRDFRQP
560 570 580 590 600
DRHPPEDFRH SSEDFRFPPE DFRHSPEDFR RPREEDFRRP SEEDFRRPWE
610 620 630 640 650
EDFRRPPEDD FRHPREEDWR RPLEEDWRRP LEEDFRRSPT EDFRQLPEED
660 670 680 690 700
FRQPPEEDLR WLPEEDFRRP PEEDWRRPPE EDFRRPLQGE WRRPPEDDFR
710 720 730 740 750
RPPEEDFRHS PEEDFRQSPQ EHFRRPPQEH FRRPPPEHFR RPPPEHFRRP
760 770 780 790 800
PPEHFRRPPP EHFRRPPPEH FRRPPPEHFR RPPQEHFRRP PQEHFRRSRE
810 820 830 840 850
EDFRHPPDED FRGPPDEDFR HPPDEDFRSP QEEDFRCPSD EDFRQLPEED
860 870 880 890 900
LREAPEEDPR LPDNFRPPGE DFRSPPDDFR SHRPFVNFGR PEGGKFDFGK
910 920 930 940 950
HNMGSFPEGR FMPDPKINCG SGRVTPIKIM NLPFKANVNE ILDFFHGYRI
960 970 980 990 1000
IPDSVSIQYN EQGLPTGEAI VAMINYNEAM AAIKDLNDRP VGPRKVKLTL

L
Length:1,001
Mass (Da):118,103
Last modified:November 25, 2008 - v2
Checksum:iA09C527B1A1EE845
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti250 – 2501S → F.
Corresponds to variant rs17853906 [ dbSNP | Ensembl ].
VAR_047291
Natural varianti605 – 6051R → C.
Corresponds to variant rs17857188 [ dbSNP | Ensembl ].
VAR_047292
Natural varianti864 – 8641N → H.
Corresponds to variant rs16916188 [ dbSNP | Ensembl ].
VAR_052219

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC010834 Genomic DNA. No translation available.
CCDSiCCDS43755.1.
RefSeqiNP_976324.2. NM_203390.2.
XP_005250972.1. XM_005250915.3.
XP_005250973.1. XM_005250916.3.
XP_011515329.1. XM_011517027.1.
XP_011515330.1. XM_011517028.1.
XP_011515331.1. XM_011517029.1.
UniGeneiHs.606916.

Genome annotation databases

EnsembliENST00000399300; ENSP00000382239; ENSG00000183808.
GeneIDi389677.
KEGGihsa:389677.
UCSCiuc003yfz.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC010834 Genomic DNA. No translation available.
CCDSiCCDS43755.1.
RefSeqiNP_976324.2. NM_203390.2.
XP_005250972.1. XM_005250915.3.
XP_005250973.1. XM_005250916.3.
XP_011515329.1. XM_011517027.1.
XP_011515330.1. XM_011517028.1.
XP_011515331.1. XM_011517029.1.
UniGeneiHs.606916.

3D structure databases

ProteinModelPortaliQ8IXT5.
SMRiQ8IXT5. Positions 146-239, 274-373, 399-486, 925-1000.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi133227. 20 interactions.
IntActiQ8IXT5. 16 interactions.
STRINGi9606.ENSP00000382239.

PTM databases

iPTMnetiQ8IXT5.
PhosphoSiteiQ8IXT5.

Polymorphism and mutation databases

BioMutaiRBM12B.
DMDMi215273872.

Proteomic databases

EPDiQ8IXT5.
MaxQBiQ8IXT5.
PaxDbiQ8IXT5.
PRIDEiQ8IXT5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000399300; ENSP00000382239; ENSG00000183808.
GeneIDi389677.
KEGGihsa:389677.
UCSCiuc003yfz.5. human.

Organism-specific databases

CTDi389677.
GeneCardsiRBM12B.
H-InvDBHIX0025665.
HGNCiHGNC:32310. RBM12B.
HPAiHPA024398.
neXtProtiNX_Q8IXT5.
PharmGKBiPA142671098.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4307. Eukaryota.
ENOG4111WZ9. LUCA.
GeneTreeiENSGT00760000119102.
HOGENOMiHOG000231575.
HOVERGENiHBG057691.
InParanoidiQ8IXT5.
OMAiEHFRRPP.
OrthoDBiEOG77DJ57.
PhylomeDBiQ8IXT5.
TreeFamiTF331899.

Miscellaneous databases

ChiTaRSiRBM12B. human.
GenomeRNAii389677.
NextBioi103029.
PROiQ8IXT5.

Gene expression databases

BgeeiQ8IXT5.
CleanExiHS_RBM12B.
ExpressionAtlasiQ8IXT5. baseline and differential.
GenevisibleiQ8IXT5. HS.

Family and domain databases

Gene3Di3.30.70.330. 5 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 5 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 5 hits.
PROSITEiPS50102. RRM. 4 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "DNA sequence and analysis of human chromosome 8."
    Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M., Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S., Asakawa T.
    , Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A., Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III, Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K., Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P., Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H., Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B., O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K., Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L., Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G., Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W., Platzer M., Shimizu N., Lander E.S.
    Nature 439:331-335(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-276; SER-278 AND SER-280, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  4. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-319, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    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.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-250; SER-254; SER-278 AND SER-638, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  6. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-278; SER-280; SER-638 AND THR-640, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-112; SER-575; SER-710 AND SER-718, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "Uncovering global SUMOylation signaling networks in a site-specific manner."
    Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M., Vertegaal A.C.
    Nat. Struct. Mol. Biol. 21:927-936(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-151, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "SUMO-2 orchestrates chromatin modifiers in response to DNA damage."
    Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V., Vertegaal A.C.
    Cell Rep. 10:1778-1791(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-151, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel small ubiquitin-like modified target proteins and acceptor lysines relevant for genome stability."
    Xiao Z., Chang J.G., Hendriks I.A., Sigurdsson J.O., Olsen J.V., Vertegaal A.C.
    Mol. Cell. Proteomics 14:1419-1434(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-151, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRB12B_HUMAN
AccessioniPrimary (citable) accession number: Q8IXT5
Secondary accession number(s): A8MYB5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2007
Last sequence update: November 25, 2008
Last modified: May 11, 2016
This is version 120 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: 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. 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.