SPEN spen family transcriptional repressor [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPENprovided by HGNC
Official Full Name: spen family transcriptional repressorprovided by HGNC
Primary source: HGNC:HGNC:17575
See related: Ensembl:ENSG00000065526 MIM:613484; AllianceGenome:HGNC:17575
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: MINT; SHARP; RATARS; RBM15C; HIAA0929
Summary: This gene encodes a hormone inducible transcriptional repressor. Repression of transcription by this gene product can occur through interactions with other repressors, by the recruitment of proteins involved in histone deacetylation, or through sequestration of transcriptional activators. The product of this gene contains a carboxy-terminal domain that permits binding to other corepressor proteins. This domain also permits interaction with members of the NuRD complex, a nucleosome remodeling protein complex that contains deacetylase activity. In addition, this repressor contains several RNA recognition motifs that confer binding to a steroid receptor RNA coactivator; this binding can modulate the activity of both liganded and nonliganded steroid receptors. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in ovary (RPKM 13.5), bone marrow (RPKM 9.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.21-p36.13

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (15847707..15940456)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (15288973..15381736)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (16174202..16266951)

Chromosome 1 - NC_000001.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.
Title: Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.
SPEN induces miR-4652-3p to target HIPK2 in nasopharyngeal carcinoma.
Title: SPEN induces miR-4652-3p to target HIPK2 in nasopharyngeal carcinoma.
SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females.
Title: SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females.
our data demonstrate a role for SPEN in the regulation of primary cilia formation and cell migration in breast cancer cells, which may collectively explain why its expression is associated with time to metastasis in cohorts of patients with ERalpha-negative breast cancers.
Title: SPEN, a new player in primary cilia formation and cell migration in breast cancer.
SPEN is a novel tumor-suppressor gene that may be clinically useful as a predictive biomarker of tamoxifen response in ERalpha-positive breast cancers.
Title: The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers.
SPEN mutations were associated with diffuse large B-cell lymphoma with hepatitis C virus infection.
Title: The NOTCH pathway is recurrently mutated in diffuse large B-cell lymphoma associated with hepatitis C virus infection.
Phosphorylation of the CK2 site on SMRT significantly increased affinity for SHARP.
Title: Structural insights into the recruitment of SMRT by the corepressor SHARP under phosphorylative regulation.
A structural study of the RNA binding properties of the RNA recognition motifs of SHARP.
Title: The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs.
These results demonstrate a role for the inactivation of SHARP transcription in DM1 biology.
Title: RNA steady-state defects in myotonic dystrophy are linked to nuclear exclusion of SHARP.
MINT3 and MINT17 were informative for patient grouping to predict local recurrence in rectal cancer patients
Title: Identification of a quantitative MINT locus methylation profile predicting local regional recurrence of rectal cancer.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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

Associated conditions

Description	Tests
Radio-Tartaglia syndrome MedGen: C5543339 OMIM: 619312 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-03-27) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2019-03-27) ClinGen Genome Curation PagePubMed

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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Replication interactions

Interaction	Pubs
Knockdown of spen homolog, transcriptional regulator (Drosophila, SPEN) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	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

SHGC-74272 (e-PCR)
- UniSTS:75274

RH45700 (e-PCR)
- UniSTS:88894

SHGC-74266 (e-PCR)
- UniSTS:13378

RH80734 (e-PCR)
- UniSTS:85060

D1S1975E (e-PCR)
- UniSTS:78670

SHGC-79191 (e-PCR)
- UniSTS:102734

RH45538 (e-PCR)
- UniSTS:26464

AL009746 (e-PCR)
- UniSTS:57441

RH48282 (e-PCR)
- UniSTS:21640

A001T05 (e-PCR)
- UniSTS:76952

G19614 (e-PCR)
- UniSTS:76953

D1S1864E (e-PCR)
- UniSTS:151008

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in random inactivation of X chromosome	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulatory ncRNA-mediated heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: msx2-interacting protein

Names: Msx2 interacting nuclear target (MINT) homolog; SMART/HDAC1-associated repressor protein; nuclear receptor transcription cofactor; spen homolog, transcriptional regulator

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.

Genomic

NG_050663.1 RefSeqGene

Range

4844..97593

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_015001.3 → NP_055816.2 msx2-interacting protein

See identical proteins and their annotated locations for NP_055816.2

Status: REVIEWED

Source sequence(s)

AF356524, AL034555, AL450998

Consensus CDS

CCDS164.1

UniProtKB/Swiss-Prot

Q96T58, Q9H9A8, Q9NWH5, Q9UQ01, Q9Y556

Related

ENSP00000364912.3, ENST00000375759.8

Conserved Domains (8) summary

COG0724
Location:8 → 81

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

cd12348
Location:7 → 81

RRM1_SHARP; RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12349
Location:336 → 409

RRM2_SHARP; RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12350
Location:436 → 509

RRM3_SHARP; RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12351
Location:510 → 586

RRM4_SHARP; RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

pfam05466
Location:1595 → 1804

BASP1; Brain acid soluble protein 1 (BASP1 protein)

pfam07744
Location:3509 → 3630

SPOC; SPOC domain

pfam15984
Location:2645 → 2723

Collagen_mid; Bacterial collagen, middle region