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Protein

RNA-binding protein 38

Gene

RBM38

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

Functioni

RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2-IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation.2 Publications

GO - Molecular functioni

  • mRNA 3'-UTR binding Source: UniProtKB
  • mRNA binding Source: UniProtKB
  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • 3'-UTR-mediated mRNA stabilization Source: UniProtKB
  • cell cycle Source: UniProtKB-KW
  • cell cycle arrest Source: UniProtKB
  • cell differentiation Source: UniProtKB-KW
  • DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest Source: UniProtKB
  • DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator Source: UniProtKB
  • mRNA processing Source: UniProtKB-KW
  • negative regulation of cell proliferation Source: UniProtKB
  • regulation of myotube differentiation Source: Ensembl
  • regulation of RNA splicing Source: UniProtKB
  • RNA splicing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Differentiation, mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 38
Alternative name(s):
CLL-associated antigen KW-5
HSRNASEB
RNA-binding motif protein 38
RNA-binding region-containing protein 1
ssDNA-binding protein SEB4
Gene namesi
Name:RBM38
Synonyms:RNPC1, SEB4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15818. RBM38.

Subcellular locationi

  • Cytoplasmcytosol 1 Publication
  • Nucleus 1 Publication

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA34449.

Polymorphism and mutation databases

BioMutaiRBM38.
DMDMi215273895.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 239239RNA-binding protein 38PRO_0000081812Add
BLAST

Proteomic databases

EPDiQ9H0Z9.
MaxQBiQ9H0Z9.
PaxDbiQ9H0Z9.
PRIDEiQ9H0Z9.

PTM databases

iPTMnetiQ9H0Z9.
PhosphoSiteiQ9H0Z9.

Expressioni

Inductioni

By p53/TP53 family. Directly induced by p53/TP53, TP63/p63 and TP73/p73.1 Publication

Gene expression databases

BgeeiQ9H0Z9.
CleanExiHS_RBM38.
ExpressionAtlasiQ9H0Z9. baseline and differential.
GenevisibleiQ9H0Z9. HS.

Organism-specific databases

HPAiCAB017036.
HPA045389.

Interactioni

Protein-protein interaction databases

BioGridi120710. 7 interactions.
IntActiQ9H0Z9. 6 interactions.
STRINGi9606.ENSP00000348538.

Structurei

Secondary structure

1
239
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi32 – 398Combined sources
Helixi47 – 559Combined sources
Beta strandi60 – 667Combined sources
Beta strandi69 – 713Combined sources
Beta strandi76 – 849Combined sources
Helixi85 – 928Combined sources
Beta strandi105 – 1095Combined sources
Turni110 – 1123Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CQDNMR-A24-126[»]
ProteinModelPortaliQ9H0Z9.
SMRiQ9H0Z9. Positions 28-126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H0Z9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini34 – 11178RRMPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the RBM38 family.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0149. Eukaryota.
ENOG4111PGT. LUCA.
GeneTreeiENSGT00390000002308.
HOVERGENiHBG108399.
InParanoidiQ9H0Z9.
OMAiTFLHYAP.
OrthoDBiEOG77M8Q4.
PhylomeDBiQ9H0Z9.
TreeFamiTF314235.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9H0Z9-1) [UniParc]FASTAAdd to basket

Also known as: RNPC1a

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
MLLQPAPCAP SAGFPRPLAA PGAMHGSQKD TTFTKIFVGG LPYHTTDASL
60 70 80 90 100
RKYFEGFGDI EEAVVITDRQ TGKSRGYGFV TMADRAAAER ACKDPNPIID
110 120 130 140 150
GRKANVNLAY LGAKPRSLQT GFAIGVQQLH PTLIQRTYGL TPHYIYPPAI
160 170 180 190 200
VQPSVVIPAA PVPSLSSPYI EYTPASPAYA QYPPATYDQY PYAASPATAA
210 220 230
SFVGYSYPAA VPQALSAAAP AGTTFVQYQA PQLQPDRMQ
Length:239
Mass (Da):25,498
Last modified:November 25, 2008 - v2
Checksum:iF20038A92C980757
GO
Isoform 2 (identifier: Q9H0Z9-2) [UniParc]FASTAAdd to basket

Also known as: RNPC1b

The sequence of this isoform differs from the canonical sequence as follows:
     122-239: Missing.

Show »
Length:121
Mass (Da):12,914
Checksum:i7A4B2F4C1B35CB0B
GO

Sequence cautioni

The sequence AAH18711.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAL99924.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAA53064.1 differs from that shown.Chimeric cDNA.Curated
The sequence EAW75522.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti15 – 151P → S in CAA53063 (Ref. 4) Curated
Sequence conflicti23 – 253AMH → VMY in CAA53063 (Ref. 4) Curated
Sequence conflicti25 – 251H → Y in CAA53063 (Ref. 4) Curated
Sequence conflicti30 – 301D → G in CAA53063 (Ref. 4) Curated
Sequence conflicti116 – 1172RS → WC in CAA53063 (Ref. 4) Curated
Sequence conflicti116 – 1172RS → WC in CAA53064 (Ref. 4) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti178 – 1781A → V.1 Publication
Corresponds to variant rs1065288 [ dbSNP | Ensembl ].
VAR_015225
Natural varianti200 – 2001A → D.1 Publication
Corresponds to variant rs1065289 [ dbSNP | Ensembl ].
VAR_015226
Natural varianti212 – 2121P → H.1 Publication
Corresponds to variant rs1065290 [ dbSNP | Ensembl ].
VAR_015227
Natural varianti226 – 2261V → L.
Corresponds to variant rs16980970 [ dbSNP | Ensembl ].
VAR_059823

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei122 – 239118Missing in isoform 2. CuratedVSP_035881Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF432218 mRNA. Translation: AAL99924.1. Different initiation.
AL109955 Genomic DNA. No translation available.
CH471077 Genomic DNA. Translation: EAW75522.1. Sequence problems.
X75314 mRNA. Translation: CAA53063.1.
X75315 mRNA. Translation: CAA53064.1. Sequence problems.
BC018711 mRNA. Translation: AAH18711.1. Different initiation.
CCDSiCCDS46617.1. [Q9H0Z9-1]
CCDS46618.1. [Q9H0Z9-2]
RefSeqiNP_001278709.1. NM_001291780.1.
NP_059965.2. NM_017495.5. [Q9H0Z9-1]
NP_906270.1. NM_183425.2. [Q9H0Z9-2]
UniGeneiHs.236361.

Genome annotation databases

EnsembliENST00000356208; ENSP00000348538; ENSG00000132819. [Q9H0Z9-1]
ENST00000440234; ENSP00000407848; ENSG00000132819. [Q9H0Z9-2]
GeneIDi55544.
KEGGihsa:55544.
UCSCiuc010zzj.3. human. [Q9H0Z9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF432218 mRNA. Translation: AAL99924.1. Different initiation.
AL109955 Genomic DNA. No translation available.
CH471077 Genomic DNA. Translation: EAW75522.1. Sequence problems.
X75314 mRNA. Translation: CAA53063.1.
X75315 mRNA. Translation: CAA53064.1. Sequence problems.
BC018711 mRNA. Translation: AAH18711.1. Different initiation.
CCDSiCCDS46617.1. [Q9H0Z9-1]
CCDS46618.1. [Q9H0Z9-2]
RefSeqiNP_001278709.1. NM_001291780.1.
NP_059965.2. NM_017495.5. [Q9H0Z9-1]
NP_906270.1. NM_183425.2. [Q9H0Z9-2]
UniGeneiHs.236361.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CQDNMR-A24-126[»]
ProteinModelPortaliQ9H0Z9.
SMRiQ9H0Z9. Positions 28-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120710. 7 interactions.
IntActiQ9H0Z9. 6 interactions.
STRINGi9606.ENSP00000348538.

PTM databases

iPTMnetiQ9H0Z9.
PhosphoSiteiQ9H0Z9.

Polymorphism and mutation databases

BioMutaiRBM38.
DMDMi215273895.

Proteomic databases

EPDiQ9H0Z9.
MaxQBiQ9H0Z9.
PaxDbiQ9H0Z9.
PRIDEiQ9H0Z9.

Protocols and materials databases

DNASUi55544.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000356208; ENSP00000348538; ENSG00000132819. [Q9H0Z9-1]
ENST00000440234; ENSP00000407848; ENSG00000132819. [Q9H0Z9-2]
GeneIDi55544.
KEGGihsa:55544.
UCSCiuc010zzj.3. human. [Q9H0Z9-1]

Organism-specific databases

CTDi55544.
GeneCardsiRBM38.
H-InvDBHIX0015939.
HGNCiHGNC:15818. RBM38.
HPAiCAB017036.
HPA045389.
MIMi612428. gene.
neXtProtiNX_Q9H0Z9.
PharmGKBiPA34449.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0149. Eukaryota.
ENOG4111PGT. LUCA.
GeneTreeiENSGT00390000002308.
HOVERGENiHBG108399.
InParanoidiQ9H0Z9.
OMAiTFLHYAP.
OrthoDBiEOG77M8Q4.
PhylomeDBiQ9H0Z9.
TreeFamiTF314235.

Miscellaneous databases

EvolutionaryTraceiQ9H0Z9.
GenomeRNAii55544.
NextBioi59995.
PROiQ9H0Z9.
SOURCEiSearch...

Gene expression databases

BgeeiQ9H0Z9.
CleanExiHS_RBM38.
ExpressionAtlasiQ9H0Z9. baseline and differential.
GenevisibleiQ9H0Z9. HS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of tumor-associated antigens in chronic lymphocytic leukemia by SEREX."
    Krackhardt A.M., Witzens M., Harig S., Hodi F.S., Zauls A.J., Chessia M., Barrett P., Gribben J.G.
    Blood 100:2123-2131(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Leukemia.
  2. "The DNA sequence and comparative analysis of human chromosome 20."
    Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
    , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
    Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "A novel murine RRM-type protein and its human homolog."
    Ruehlmann A., Gupta A., Terhorst C.
    Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 11-239, VARIANTS VAL-178; ASP-200 AND HIS-212.
    Tissue: Thymus.
  5. "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] OF 23-239.
    Tissue: Tonsil.
  6. "RNPC1, an RNA-binding protein and a target of the p53 family, is required for maintaining the stability of the basal and stress-induced p21 transcript."
    Shu L., Yan W., Chen X.
    Genes Dev. 20:2961-2972(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ALTERNATIVE SPLICING (ISOFORMS 1 AND 2), RNA-BINDING, SUBCELLULAR LOCATION, INDUCTION.
  7. "ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing."
    Warzecha C.C., Sato T.K., Nabet B., Hogenesch J.B., Carstens R.P.
    Mol. Cell 33:591-601(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Solution structure of the RNA recognition motif in RNA-binding region containing protein 1."
    RIKEN structural genomics initiative (RSGI)
    Submitted (MAY-2005) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 24-126.

Entry informationi

Entry nameiRBM38_HUMAN
AccessioniPrimary (citable) accession number: Q9H0Z9
Secondary accession number(s): A6NDK1
, A6NMU6, Q15350, Q15351, Q9BYK3, Q9BYK4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2003
Last sequence update: November 25, 2008
Last modified: March 16, 2016
This is version 133 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

Caution

It is uncertain whether Met-1 or Met-24 is the initiator.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.