RBM23 RNA binding motif protein 23 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RBM23provided by HGNC
Official Full Name: RNA binding motif protein 23provided by HGNC
Primary source: HGNC:HGNC:20155
See related: Ensembl:ENSG00000100461 AllianceGenome:HGNC:20155
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PP239; RNPC4; CAPERbeta
Summary: This gene encodes a member of the U2AF-like family of RNA binding proteins. This protein interacts with some steroid nuclear receptors, localizes to the promoter of a steroid- responsive gene, and increases transcription of steroid-responsive transcriptional reporters in a hormone-dependent manner. It is also implicated in the steroid receptor-dependent regulation of alternative splicing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 14.7), ovary (RPKM 12.8) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 14q11.2

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (22893204..22919149, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (17091268..17117229, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (23362413..23388358, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RBM23 Drives Hepatocellular Carcinoma by Activating NF-kappaB Signaling Pathway.
Title: RBM23 Drives Hepatocellular Carcinoma by Activating NF-κB Signaling Pathway.
aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and the closely related splicing factor RBM23 without the requirement for a high-affinity ligand
Title: Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D14S1223 (e-PCR)
- UniSTS:81177

RH123339 (e-PCR)
- UniSTS:135716

SHGC-32250 (e-PCR)
- UniSTS:35679

G21627 (e-PCR)
- UniSTS:2930

D15S1477 (e-PCR)
- UniSTS:474482

IB864 (e-PCR)
- UniSTS:8092

RH78387 (e-PCR)
- UniSTS:27070

A002Q41 (e-PCR)
- UniSTS:26879

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables U1 snRNP binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: probable RNA-binding protein 23

Names: CAPER beta; RNA-binding region (RNP1, RRM) containing 4; RNA-binding region-containing protein 4; coactivator of activating protein-1 and estrogen recep- tors beta; splicing factor SF2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001077351.2 → NP_001070819.1 probable RNA-binding protein 23 isoform 1

See identical proteins and their annotated locations for NP_001070819.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AL135998, BC106012, BX161440, CK003276

Consensus CDS

CCDS41921.1

UniProtKB/Swiss-Prot

D3DS32, Q86U06, Q8ND16, Q8TB88, Q8WY40, Q9BUJ1, Q9NVV7

UniProtKB/TrEMBL

A0A0S2Z5D9, B2RDP1

Related

ENSP00000352956.3, ENST00000359890.8

Conserved Domains (1) summary

TIGR01622
Location:99 → 438

SF-CC1; splicing factor, CC1-like family
NM_001077352.2 → NP_001070820.1 probable RNA-binding protein 23 isoform 3

See identical proteins and their annotated locations for NP_001070820.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons, compared to variant 1. The resulting protein (isoform 3) is shorter than isoform 1.

Source sequence(s)

AK001344, AL132780, AL135998, BC106012, CK003276

Consensus CDS

CCDS41919.1

UniProtKB/TrEMBL

A0A0S2Z5I1, B2RDP1

Related

ENSP00000339220.5, ENST00000346528.9

Conserved Domains (3) summary

cd12284
Location:231 → 303

RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

cd12537
Location:131 → 215

RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

pfam15519
Location:324 → 404

RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein
NM_001308044.2 → NP_001294973.1 probable RNA-binding protein 23 isoform 4

See identical proteins and their annotated locations for NP_001294973.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and lacks two exons in the 5' coding region, which results in use of a downstream start codon compared to variant 1. It encodes isoform 4, which has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AA987387, AK303668, AL135998, BX161440, DC363343

Consensus CDS

CCDS76658.1

UniProtKB/TrEMBL

G3XAP0

Related

ENSP00000438504.2, ENST00000542016.6

Conserved Domains (1) summary

TIGR01622
Location:1 → 268

SF-CC1; splicing factor, CC1-like family
NM_001352762.2 → NP_001339691.1 probable RNA-binding protein 23 isoform 4

Status: REVIEWED

Source sequence(s)

AL132780, AL135998

Consensus CDS

CCDS76658.1

UniProtKB/TrEMBL

G3XAP0

Conserved Domains (1) summary

TIGR01622
Location:1 → 268

SF-CC1; splicing factor, CC1-like family
NM_001352763.2 → NP_001339692.1 probable RNA-binding protein 23 isoform 1

Status: REVIEWED

Source sequence(s)

AL132780, AL135998

Consensus CDS

CCDS41921.1

UniProtKB/Swiss-Prot

D3DS32, Q86U06, Q8ND16, Q8TB88, Q8WY40, Q9BUJ1, Q9NVV7

UniProtKB/TrEMBL

A0A0S2Z5D9, B2RDP1

Conserved Domains (1) summary

TIGR01622
Location:99 → 438

SF-CC1; splicing factor, CC1-like family
NM_001352764.2 → NP_001339693.1 probable RNA-binding protein 23 isoform 5

Status: REVIEWED

Source sequence(s)

AL132780, AL135998

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (1) summary

cl25887
Location:143 → 482

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
NM_001352765.2 → NP_001339694.1 probable RNA-binding protein 23 isoform 2

Status: REVIEWED

Source sequence(s)

AL132780, AL135998

Consensus CDS

CCDS41920.1

UniProtKB/TrEMBL

A0A0S2Z5J3, B2RDP1

Conserved Domains (1) summary

cl25887
Location:69 → 422

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
NM_001352766.2 → NP_001339695.1 probable RNA-binding protein 23 isoform 1

Status: REVIEWED

Source sequence(s)

AL132780, AL135998

Consensus CDS

CCDS41921.1

UniProtKB/Swiss-Prot

D3DS32, Q86U06, Q8ND16, Q8TB88, Q8WY40, Q9BUJ1, Q9NVV7

UniProtKB/TrEMBL

A0A0S2Z5D9, B2RDP1

Conserved Domains (1) summary

TIGR01622
Location:99 → 438

SF-CC1; splicing factor, CC1-like family
NM_018107.5 → NP_060577.3 probable RNA-binding protein 23 isoform 2

See identical proteins and their annotated locations for NP_060577.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.

Source sequence(s)

AL135998, BC024208, BC106012, CK003276

Consensus CDS

CCDS41920.1

UniProtKB/TrEMBL

A0A0S2Z5J3, B2RDP1

Related

ENSP00000382806.2, ENST00000399922.6

Conserved Domains (1) summary

cl25887
Location:69 → 422

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

22893204..22919149 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011536906.2 → XP_011535208.1 probable RNA-binding protein 23 isoform X8

See identical proteins and their annotated locations for XP_011535208.1

UniProtKB/TrEMBL

G3XAP0

Conserved Domains (1) summary

TIGR01622
Location:1 → 268

SF-CC1; splicing factor, CC1-like family
XM_011536903.2 → XP_011535205.1 probable RNA-binding protein 23 isoform X8

See identical proteins and their annotated locations for XP_011535205.1

UniProtKB/TrEMBL

G3XAP0

Conserved Domains (1) summary

TIGR01622
Location:1 → 268

SF-CC1; splicing factor, CC1-like family
XM_011536902.2 → XP_011535204.1 probable RNA-binding protein 23 isoform X8

See identical proteins and their annotated locations for XP_011535204.1

UniProtKB/TrEMBL

G3XAP0

Conserved Domains (1) summary

TIGR01622
Location:1 → 268

SF-CC1; splicing factor, CC1-like family
XM_011536895.4 → XP_011535197.1 probable RNA-binding protein 23 isoform X4

See identical proteins and their annotated locations for XP_011535197.1

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (4) summary

cd12284
Location:275 → 347

RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

cd12537
Location:175 → 259

RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

pfam13900
Location:6 → 41

GVQW; Putative domain of unknown function

pfam15519
Location:368 → 448

RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein
XM_011536892.3 → XP_011535194.1 probable RNA-binding protein 23 isoform X1

See identical proteins and their annotated locations for XP_011535194.1

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (1) summary

TIGR01622
Location:113 → 466

SF-CC1; splicing factor, CC1-like family
XM_011536894.3 → XP_011535196.1 probable RNA-binding protein 23 isoform X3

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (4) summary

cd12284
Location:291 → 363

RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

cd12537
Location:191 → 275

RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

pfam13900
Location:6 → 41

GVQW; Putative domain of unknown function

pfam15519
Location:384 → 464

RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein
XM_011536897.3 → XP_011535199.1 probable RNA-binding protein 23 isoform X6

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (3) summary

cd12284
Location:267 → 339

RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

cd12537
Location:167 → 251

RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

pfam15519
Location:360 → 440

RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein
XM_047431521.1 → XP_047287477.1 probable RNA-binding protein 23 isoform X8

UniProtKB/TrEMBL

G3XAP0
XM_011536896.3 → XP_011535198.1 probable RNA-binding protein 23 isoform X5

See identical proteins and their annotated locations for XP_011535198.1

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (4) summary

cd12284
Location:275 → 347

RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

cd12537
Location:175 → 259

RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

pfam13900
Location:6 → 41

GVQW; Putative domain of unknown function

pfam15519
Location:368 → 448

RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein
XM_011536893.4 → XP_011535195.1 probable RNA-binding protein 23 isoform X2

See identical proteins and their annotated locations for XP_011535195.1

UniProtKB/TrEMBL

B2RDP1

Conserved Domains (1) summary

TIGR01622
Location:113 → 466

SF-CC1; splicing factor, CC1-like family
XM_024449644.2 → XP_024305412.1 probable RNA-binding protein 23 isoform X7

UniProtKB/TrEMBL

B3KWQ8

Conserved Domains (1) summary

cl25887
Location:143 → 356

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

17091268..17117229 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054376291.1 → XP_054232266.1 probable RNA-binding protein 23 isoform X8

UniProtKB/TrEMBL

B7Z8M4
XM_054376290.1 → XP_054232265.1 probable RNA-binding protein 23 isoform X8

UniProtKB/TrEMBL

B7Z8M4
XM_054376293.1 → XP_054232268.1 probable RNA-binding protein 23 isoform X8

UniProtKB/TrEMBL

B7Z8M4
XM_054376287.1 → XP_054232262.1 probable RNA-binding protein 23 isoform X4
XM_054376284.1 → XP_054232259.1 probable RNA-binding protein 23 isoform X1
XM_054376286.1 → XP_054232261.1 probable RNA-binding protein 23 isoform X3
XM_054376292.1 → XP_054232267.1 probable RNA-binding protein 23 isoform X8

UniProtKB/TrEMBL

B7Z8M4
XM_054376288.1 → XP_054232263.1 probable RNA-binding protein 23 isoform X5
XM_054376285.1 → XP_054232260.1 probable RNA-binding protein 23 isoform X2
XM_054376289.1 → XP_054232264.1 probable RNA-binding protein 23 isoform X7