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Protein

RNA-binding protein 47

Gene

RBM47

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

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 47
Alternative name(s):
RNA-binding motif protein 47
Gene namesi
Name:RBM47
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:30358. RBM47.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162400825.

Polymorphism and mutation databases

BioMutaiRBM47.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 593593RNA-binding protein 47PRO_0000307855Add
BLAST

Proteomic databases

EPDiA0AV96.
MaxQBiA0AV96.
PaxDbiA0AV96.
PRIDEiA0AV96.

PTM databases

iPTMnetiA0AV96.
PhosphoSiteiA0AV96.

Expressioni

Gene expression databases

BgeeiA0AV96.
CleanExiHS_RBM47.
ExpressionAtlasiA0AV96. baseline and differential.
GenevisibleiA0AV96. HS.

Organism-specific databases

HPAiHPA006347.

Interactioni

Protein-protein interaction databases

BioGridi119998. 5 interactions.
IntActiA0AV96. 4 interactions.
MINTiMINT-4654833.
STRINGi9606.ENSP00000295971.

Structurei

Secondary structure

1
593
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi150 – 1567Combined sources
Helixi164 – 17411Combined sources
Beta strandi178 – 1825Combined sources
Beta strandi185 – 1873Combined sources
Turni189 – 1935Combined sources
Beta strandi196 – 2038Combined sources
Helixi204 – 2118Combined sources
Turni212 – 2165Combined sources
Beta strandi227 – 2315Combined sources
Turni237 – 2393Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DISNMR-A150-245[»]
ProteinModelPortaliA0AV96.
SMRiA0AV96. Positions 72-322.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA0AV96.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini71 – 14979RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini151 – 23383RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini246 – 31873RRM 3PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi487 – 58195Ala-richAdd
BLAST

Sequence similaritiesi

Belongs to the RRM RBM47 family.Curated
Contains 3 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0117. Eukaryota.
ENOG410XTJ5. LUCA.
GeneTreeiENSGT00550000074366.
HOGENOMiHOG000186083.
HOVERGENiHBG051917.
InParanoidiA0AV96.
OMAiIGPNREY.
OrthoDBiEOG73JKW2.
PhylomeDBiA0AV96.
TreeFamiTF314932.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR006535. HnRNP_R/Q_splicing_fac.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 3 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01648. hnRNP-R-Q. 1 hit.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: A0AV96-1) [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
MTAEDSTAAM SSDSAAGSSA KVPEGVAGAP NEAALLALME RTGYSMVQEN
60 70 80 90 100
GQRKYGGPPP GWEGPHPQRG CEVFVGKIPR DVYEDELVPV FEAVGRIYEL
110 120 130 140 150
RLMMDFDGKN RGYAFVMYCH KHEAKRAVRE LNNYEIRPGR LLGVCCSVDN
160 170 180 190 200
CRLFIGGIPK MKKREEILEE IAKVTEGVLD VIVYASAADK MKNRGFAFVE
210 220 230 240 250
YESHRAAAMA RRKLMPGRIQ LWGHQIAVDW AEPEIDVDED VMETVKILYV
260 270 280 290 300
RNLMIETTED TIKKSFGQFN PGCVERVKKI RDYAFVHFTS REDAVHAMNN
310 320 330 340 350
LNGTELEGSC LEVTLAKPVD KEQYSRYQKA ARGGGAAEAA QQPSYVYSCD
360 370 380 390 400
PYTLAYYGYP YNALIGPNRD YFVKAGSIRG RGRGAAGNRA PGPRGSYLGG
410 420 430 440 450
YSAGRGIYSR YHEGKGKQQE KGYELVPNLE IPTVNPVAIK PGTVAIPAIG
460 470 480 490 500
AQYSMFPAAP APKMIEDGKI HTVEHMISPI AVQPDPASAA AAAAAAAAAA
510 520 530 540 550
AAVIPTVSTP PPFQGRPITP VYTVAPNVQR IPTAGIYGAS YVPFAAPATA
560 570 580 590
TIATLQKNAA AAAAMYGGYA GYIPQAFPAA AIQVPIPDVY QTY
Length:593
Mass (Da):64,099
Last modified:November 30, 2010 - v2
Checksum:iAEA061F89A68010B
GO
Isoform 2 (identifier: A0AV96-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     375-443: Missing.

Show »
Length:524
Mass (Da):56,920
Checksum:i4C7004D92117D5B1
GO

Sequence cautioni

The sequence AAM21973.1 differs from that shown. Reason: Frameshift at positions 561 and 577. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti9 – 91A → T in AAM21973 (Ref. 1) Curated
Sequence conflicti97 – 971I → T in BAA91049 (PubMed:14702039).Curated
Sequence conflicti515 – 5151G → V in AAM21972 (Ref. 1) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti538 – 5381G → R.
Corresponds to variant rs35529250 [ dbSNP | Ensembl ].
VAR_061832
Natural varianti565 – 5651M → V.2 Publications
Corresponds to variant rs278981 [ dbSNP | Ensembl ].
VAR_054770

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei375 – 44369Missing in isoform 2. 1 PublicationVSP_028839Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF261889 Genomic DNA. Translation: AAM21972.1.
AF262323 mRNA. Translation: AAM21973.1. Frameshift.
AK000280 mRNA. Translation: BAA91049.1.
AC098869 Genomic DNA. No translation available.
AC112717 Genomic DNA. No translation available.
BC034402 mRNA. Translation: AAH34402.1.
BC126261 mRNA. Translation: AAI26262.1.
CCDSiCCDS3460.1. [A0AV96-2]
CCDS43223.1. [A0AV96-1]
RefSeqiNP_001092104.1. NM_001098634.1. [A0AV96-1]
NP_061900.2. NM_019027.3. [A0AV96-2]
XP_005248160.1. XM_005248103.2. [A0AV96-1]
XP_005248164.1. XM_005248107.2. [A0AV96-1]
XP_005248165.1. XM_005248108.2. [A0AV96-1]
XP_005248166.1. XM_005248109.3. [A0AV96-1]
XP_011512004.1. XM_011513702.1. [A0AV96-1]
XP_011512005.1. XM_011513703.1. [A0AV96-1]
XP_011512006.1. XM_011513704.1. [A0AV96-1]
XP_011512007.1. XM_011513705.1. [A0AV96-1]
XP_011512008.1. XM_011513706.1. [A0AV96-1]
XP_011512009.1. XM_011513707.1. [A0AV96-1]
XP_011512010.1. XM_011513708.1. [A0AV96-1]
XP_011512012.1. XM_011513710.1. [A0AV96-2]
UniGeneiHs.518727.

Genome annotation databases

EnsembliENST00000295971; ENSP00000295971; ENSG00000163694. [A0AV96-1]
ENST00000381793; ENSP00000371212; ENSG00000163694. [A0AV96-1]
ENST00000381795; ENSP00000371214; ENSG00000163694. [A0AV96-2]
GeneIDi54502.
KEGGihsa:54502.
UCSCiuc003gvc.3. human. [A0AV96-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF261889 Genomic DNA. Translation: AAM21972.1.
AF262323 mRNA. Translation: AAM21973.1. Frameshift.
AK000280 mRNA. Translation: BAA91049.1.
AC098869 Genomic DNA. No translation available.
AC112717 Genomic DNA. No translation available.
BC034402 mRNA. Translation: AAH34402.1.
BC126261 mRNA. Translation: AAI26262.1.
CCDSiCCDS3460.1. [A0AV96-2]
CCDS43223.1. [A0AV96-1]
RefSeqiNP_001092104.1. NM_001098634.1. [A0AV96-1]
NP_061900.2. NM_019027.3. [A0AV96-2]
XP_005248160.1. XM_005248103.2. [A0AV96-1]
XP_005248164.1. XM_005248107.2. [A0AV96-1]
XP_005248165.1. XM_005248108.2. [A0AV96-1]
XP_005248166.1. XM_005248109.3. [A0AV96-1]
XP_011512004.1. XM_011513702.1. [A0AV96-1]
XP_011512005.1. XM_011513703.1. [A0AV96-1]
XP_011512006.1. XM_011513704.1. [A0AV96-1]
XP_011512007.1. XM_011513705.1. [A0AV96-1]
XP_011512008.1. XM_011513706.1. [A0AV96-1]
XP_011512009.1. XM_011513707.1. [A0AV96-1]
XP_011512010.1. XM_011513708.1. [A0AV96-1]
XP_011512012.1. XM_011513710.1. [A0AV96-2]
UniGeneiHs.518727.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DISNMR-A150-245[»]
ProteinModelPortaliA0AV96.
SMRiA0AV96. Positions 72-322.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119998. 5 interactions.
IntActiA0AV96. 4 interactions.
MINTiMINT-4654833.
STRINGi9606.ENSP00000295971.

PTM databases

iPTMnetiA0AV96.
PhosphoSiteiA0AV96.

Polymorphism and mutation databases

BioMutaiRBM47.

Proteomic databases

EPDiA0AV96.
MaxQBiA0AV96.
PaxDbiA0AV96.
PRIDEiA0AV96.

Protocols and materials databases

DNASUi54502.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000295971; ENSP00000295971; ENSG00000163694. [A0AV96-1]
ENST00000381793; ENSP00000371212; ENSG00000163694. [A0AV96-1]
ENST00000381795; ENSP00000371214; ENSG00000163694. [A0AV96-2]
GeneIDi54502.
KEGGihsa:54502.
UCSCiuc003gvc.3. human. [A0AV96-1]

Organism-specific databases

CTDi54502.
GeneCardsiRBM47.
HGNCiHGNC:30358. RBM47.
HPAiHPA006347.
neXtProtiNX_A0AV96.
PharmGKBiPA162400825.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0117. Eukaryota.
ENOG410XTJ5. LUCA.
GeneTreeiENSGT00550000074366.
HOGENOMiHOG000186083.
HOVERGENiHBG051917.
InParanoidiA0AV96.
OMAiIGPNREY.
OrthoDBiEOG73JKW2.
PhylomeDBiA0AV96.
TreeFamiTF314932.

Miscellaneous databases

ChiTaRSiRBM47. human.
EvolutionaryTraceiA0AV96.
GenomeRNAii54502.
PROiA0AV96.

Gene expression databases

BgeeiA0AV96.
CleanExiHS_RBM47.
ExpressionAtlasiA0AV96. baseline and differential.
GenevisibleiA0AV96. HS.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR006535. HnRNP_R/Q_splicing_fac.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 3 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01648. hnRNP-R-Q. 1 hit.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "SPICE cloning and characterization of a human cDNA encoding a novel RNA-binding protein."
    Wang A., Gonzalez-Santos J.M., Hu J.
    Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).
    Tissue: Lung.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    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.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT VAL-565.
  3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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 1), VARIANT VAL-565.
    Tissue: Brain.
  5. "Solution structure of the RRM domain of unnamed protein product."
    RIKEN structural genomics initiative (RSGI)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 150-245.

Entry informationi

Entry nameiRBM47_HUMAN
AccessioniPrimary (citable) accession number: A0AV96
Secondary accession number(s): A0PJK2
, B5MED4, Q8NI52, Q8NI53, Q9NXG3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 23, 2007
Last sequence update: November 30, 2010
Last modified: June 8, 2016
This is version 84 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. 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.