RTRAF RNA transcription, translation and transport factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: RTRAFprovided by HGNC
Official Full Name: RNA transcription, translation and transport factorprovided by HGNC
Primary source: HGNC:HGNC:23169
See related: Ensembl:ENSG00000087302 MIM:610858; AllianceGenome:HGNC:23169
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: CLE; CLE7; hCLE; CGI99; RLLM1; hCLE1; CGI-99; LCRP369; C14orf166
Summary: Enables RNA binding activity; RNA polymerase II complex binding activity; and identical protein binding activity. Involved in negative regulation of protein kinase activity; positive regulation of transcription by RNA polymerase II; and tRNA splicing, via endonucleolytic cleavage and ligation. Located in microtubule cytoskeleton; nucleoplasm; and perinuclear region of cytoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis (RPKM 109.7), fat (RPKM 62.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q22.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (51989546..52010694)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (46196590..46217738)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (52456264..52477412)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast-two-hybrid screening data.
Title: An in silico prediction of interaction models of influenza A virus PA and human C14orf166 protein from yeast-two-hybrid screening data.
Molecular architecture of the human tRNA ligase complex.
Title: Molecular architecture of the human tRNA ligase complex.
the two structural homologs FAM98A and FAM98B included in a novel complex with DDX1 and C14orf166 are required for PRMT1 expression in colorectal cancer cell lines
Title: FAM98A associates with DDX1-C14orf166-FAM98B in a novel complex involved in colorectal cancer progression.
C14ORF166 may represent a biomarker of pelvic lymph node metastasis in uterine cervical cancer
Title: C14ORF166 overexpression is associated with pelvic lymph node metastasis and poor prognosis in uterine cervical cancer.
C14orf166, a cellular protein required for viral replication, is incorporated into influenza virus particles.
Title: hCLE/C14orf166, a cellular protein required for viral replication, is incorporated into influenza virus particles.
C14orf166 promotes bladder cancer cell proliferation and can be a novel prognostic biomarker for patients with bladder cancer.
Title: C14orf166 is a high-risk biomarker for bladder cancer and promotes bladder cancer cell proliferation.
C14orf166 could be a novel prognostic biomarker of breast cancer, it also contributes to cell proliferation by regulating G1/S transition.
Title: C14orf166 overexpression correlates with tumor progression and poor prognosis of breast cancer.
Overexpression of chromosome 14 open reading frame 166 correlates with disease progression in nasopharyngeal carcinoma.
Title: Overexpression of chromosome 14 open reading frame 166 correlates with disease progression and poorer prognosis in human NPC.
hCLE/C14orf166 associates with DDX1, HSPC117, and FAM98B in a novel transcription-dependent shuttling RNA-transporting complex.
Title: hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex.
Silencing of CLE causes reduction of influenza A virus polymerase activity, viral RNA transcription and replication, virus titer, and viral particle production.
Title: Cellular human CLE/C14orf166 protein interacts with influenza virus polymerase and is required for viral replication.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, chromosome 14 open reading frame 166 (C14orf166), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with C14orf166 is increased by RRE	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G48195 (e-PCR)
- UniSTS:95292

SHGC-132026 (e-PCR)
- UniSTS:170608

UniSTS:235896 (e-PCR)
- UniSTS:235896

HUM0S17C09 (e-PCR)
- UniSTS:5265

D14S1201 (e-PCR)
- UniSTS:78514

D14S1197 (e-PCR)
- UniSTS:37317

D14S643E (e-PCR)
- UniSTS:151546

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II complex binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA transport	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of protein kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in mitotic spindle	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of tRNA-splicing ligase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of tRNA-splicing ligase complex	IDA Inferred from Direct Assay more info	PubMed
part_of tRNA-splicing ligase complex	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: RNA transcription, translation and transport factor protein

Names: CLE7 homolog; RLL motif containing 1; UPF0568 protein C14orf166

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.