NCBP3 nuclear cap binding subunit 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NCBP3provided by HGNC
Official Full Name: nuclear cap binding subunit 3provided by HGNC
Primary source: HGNC:HGNC:24612
See related: Ensembl:ENSG00000074356 MIM:616624; AllianceGenome:HGNC:24612
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ELG; C17orf85; HSA277841
Summary: Enables RNA 7-methylguanosine cap binding activity and mRNA binding activity. Involved in defense response to virus. Located in cytoplasm and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bone marrow (RPKM 6.9), placenta (RPKM 6.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (3802158..3846246, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (3690835..3734921, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (3705452..3749540, complement)

Chromosome 17 - NC_000017.11 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?

NCBP3/SNHG6 inhibits GBX2 transcription in a histone modification manner to facilitate the malignant biological behaviour of glioma cells.
Title: NCBP3/SNHG6 inhibits GBX2 transcription in a histone modification manner to facilitate the malignant biological behaviour of glioma cells.
NCBP3 positively impacts mRNA biogenesis.
Title: NCBP3 positively impacts mRNA biogenesis.
Affinity proteomic dissection of the human nuclear cap-binding complex interactome.
Title: Affinity proteomic dissection of the human nuclear cap-binding complex interactome.
NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to poly(A) RNA export. Study proposes the existence of an alternative cap-binding complex involving NCBP1 and NCBP3 that plays a key role in mRNA biogenesis.
Title: mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3.

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

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

D15S1477 (e-PCR)
- UniSTS:474482

WI-11637 (e-PCR)
- UniSTS:62339

D9S1767 (e-PCR)
- UniSTS:154244

WI-22144 (e-PCR)
- UniSTS:46531

STS-H93344 (e-PCR)
- UniSTS:42985

HSA277841__6597 (e-PCR)
- UniSTS:468465

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA 7-methylguanosine cap binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA cap binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in 7-methylguanosine mRNA capping	IEA Inferred from Electronic Annotation more info
involved_in defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in regulatory ncRNA-mediated post-transcriptional gene silencing	NAS Non-traceable Author Statement more info	PubMed
involved_in snRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of RNA cap binding complex	TAS Traceable Author Statement more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear cap binding complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nuclear cap-binding protein subunit 3

Names: CTD-3195I5.1; CTD-3195I5.5

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_001114118.3 → NP_001107590.1 nuclear cap-binding protein subunit 3 isoform 1

See identical proteins and their annotated locations for NP_001107590.1

Status: VALIDATED

Source sequence(s)

AC116914, AJ277841, BM974475, BP344033, DA403386, DA815746, KC877633, KC877636

Consensus CDS

CCDS45578.1

UniProtKB/Swiss-Prot

B3KWG7, Q53F19, Q7L406, Q96FK1, Q9NXZ4

Related

ENSP00000373657.4, ENST00000389005.6

Conserved Domains (1) summary

pfam10309
Location:123 → 177

NCBP3; Nuclear cap-binding protein subunit 3
NM_001398494.1 → NP_001385423.1 nuclear cap-binding protein subunit 3 isoform 2

Status: VALIDATED

Source sequence(s)

AC005940, AC116914, KC877633, KC877636

Conserved Domains (1) summary

pfam10309
Location:123 → 177

NCBP3; Nuclear cap-binding protein subunit 3

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_000017.11 Reference GRCh38.p14 Primary Assembly

Range

3802158..3846246 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_007065313.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

3690835..3734921 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_008484858.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_018553.3: Suppressed sequence

Description

NM_018553.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein, and the transcript is a candidate for nonsense-mediated mRNA decay (NMD) if the expected exon 1 start codon is used.