Spen spen family transcription repressor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Spenprovided by MGI
Official Full Name: spen family transcription repressorprovided by MGI
Primary source: MGI:MGI:1891706
See related: Ensembl:ENSMUSG00000040761 AllianceGenome:MGI:1891706
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Mint; mKIAA0929
Summary: Enables DNA-binding transcription factor activity; single-stranded DNA binding activity; and transcription corepressor activity. Involved in random inactivation of X chromosome. Acts upstream of or within negative regulation of DNA-templated transcription and positive regulation of DNA-templated transcription. Located in nucleus. Is expressed in central nervous system; genitourinary system; hemolymphoid system; sensory organ; and tooth. Human ortholog(s) of this gene implicated in esophagus squamous cell carcinoma. Orthologous to human SPEN (spen family transcriptional repressor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in thymus adult (RPKM 10.9), adrenal adult (RPKM 8.5) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 D3; 4 74.26 cM

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (141195199..141265955, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (141467885..141538644, complement)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA-binding protein SPEN controls hepatocyte maturation via regulating Hnf4alpha expression during liver development.
Title: RNA-binding protein SPEN controls hepatocyte maturation via regulating Hnf4α expression during liver development.
SPEN is required for Xist upregulation during initiation of X chromosome inactivation.
Title: SPEN is required for Xist upregulation during initiation of X chromosome inactivation.
Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading.
Title: Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading.
Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
Title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity.
Title: Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity.
SPEN is a key orchestrator of X-chromosome inactivation (XCI) in vivo and its mechanism of action is elucidated; SPEN acts as a molecular integrator for the initiation of XCI, bridging Xist RNA with the transcription machinery--as well as with nucleosome remodellers and histone deacetylases-at active enhancers and promoters
Title: SPEN integrates transcriptional and epigenetic control of X-inactivation.
Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site.
Title: Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site.
Spenito, a small Spen family member, counteracted Spen function in fat regulation. Finally, mouse Spen and Spenito transcript levels scaled directly with body fat in vivo, suggesting a conserved role in fat liberation and catabolism. This study demonstrates that Spen is a key regulator of energy balance and provides a molecular context to understand the metabolic defects that arise from Spen dysfunction.
Title: An autonomous metabolic role for Spen.
Spen is required for Xist-mediated silencing.
Title: A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing.
Spen is required for gene repression by Xist. Spen is not required for Xist RNA localization and the recruitment of chromatin modifications.
Title: Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SGC33756 (e-PCR)
- UniSTS:32009

Spen (e-PCR), detects polymorphism
- UniSTS:479042

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
NOT enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info

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

Component	Evidence Code	Pubs
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: msx2-interacting protein

Names: Msx2 interacting nuclear target protein; SMART/HDAC1-associated repressor protein; 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.

mRNA and Protein(s)

NM_001347235.1 → NP_001334164.1 msx2-interacting protein isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL670285, AL670446

Consensus CDS

CCDS84815.1

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

UniProtKB/TrEMBL

A2ADB1

Related

ENSMUSP00000077925.4, ENSMUST00000078886.10
NM_019763.2 → NP_062737.2 msx2-interacting protein isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AF156529, AK137647, AL670285, BY726481

Consensus CDS

CCDS38940.1

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

UniProtKB/TrEMBL

A2ADB0

Related

ENSMUSP00000101412.3, ENSMUST00000105786.3

Conserved Domains (9) summary

COG0724
Location:8 → 145

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:338 → 411

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

cd12350
Location:438 → 511

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

cd12351
Location:512 → 588

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

TIGR01642
Location:128 → 596

U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

pfam05466
Location:1611 → 1834

BASP1; Brain acid soluble protein 1 (BASP1 protein)

pfam07744
Location:3488 → 3609

SPOC; SPOC domain

pfam15984
Location:2641 → 2722

Collagen_mid; Bacterial collagen, middle region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

141195199..141265955 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036164267.1 → XP_036020160.1 msx2-interacting protein isoform X4

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

Conserved Domains (8) summary

PTZ00121
Location:580 → 1211

PTZ00121; MAEBL; Provisional

PHA03247
Location:1568 → 2002

PHA03247; large tegument protein UL36; Provisional

pfam07744
Location:3420 → 3583

SPOC; SPOC domain

pfam15984
Location:2580 → 2658

Collagen_mid; Bacterial collagen, middle region

cd12348
Location:7 → 81

RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12349
Location:338 → 411

RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12350
Location:438 → 511

RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cl17169
Location:512 → 571

RRM_SF; RNA recognition motif (RRM) superfamily
XM_036164266.1 → XP_036020159.1 msx2-interacting protein isoform X3

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

Conserved Domains (8) summary

PTZ00121
Location:597 → 1234

PTZ00121; MAEBL; Provisional

PHA03247
Location:1591 → 2025

PHA03247; large tegument protein UL36; Provisional

pfam07744
Location:3443 → 3606

SPOC; SPOC domain

pfam15984
Location:2603 → 2681

Collagen_mid; Bacterial collagen, middle region

cd12348
Location:7 → 81

RRM1_SHARP; RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12349
Location:338 → 411

RRM2_SHARP; RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12350
Location:438 → 511

RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cl17169
Location:512 → 571

RRM_SF; RNA recognition motif (RRM) superfamily
XM_006539070.4 → XP_006539133.1 msx2-interacting protein isoform X2

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

Conserved Domains (9) summary

PTZ00121
Location:618 → 1249

PTZ00121; MAEBL; Provisional

PHA03247
Location:1606 → 2040

PHA03247; large tegument protein UL36; Provisional

cd12348
Location:7 → 81

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

cd12349
Location:338 → 411

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

cd12350
Location:438 → 511

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

cd12351
Location:512 → 588

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

TIGR01642
Location:128 → 596

U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

pfam07744
Location:3460 → 3619

SPOC; SPOC domain

pfam15984
Location:2618 → 2699

Collagen_mid; Bacterial collagen, middle region
XM_006539073.5 → XP_006539136.1 msx2-interacting protein isoform X5

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

Conserved Domains (8) summary

PTZ00121
Location:635 → 1272

PTZ00121; MAEBL; Provisional

PHA03247
Location:1629 → 2063

PHA03247; large tegument protein UL36; Provisional

cd12348
Location:7 → 81

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

cd12349
Location:338 → 411

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

cd12350
Location:438 → 511

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

cd12351
Location:512 → 588

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

TIGR01642
Location:128 → 596

U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

pfam07744
Location:3360 → 3519

SPOC; SPOC domain
XM_006539069.4 → XP_006539132.1 msx2-interacting protein isoform X1

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

Conserved Domains (9) summary

PTZ00121
Location:635 → 1272

PTZ00121; MAEBL; Provisional

PHA03247
Location:1629 → 2063

PHA03247; large tegument protein UL36; Provisional

cd12348
Location:7 → 81

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

cd12349
Location:338 → 411

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

cd12350
Location:438 → 511

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

cd12351
Location:512 → 588

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

TIGR01642
Location:128 → 596

U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

pfam07744
Location:3483 → 3642

SPOC; SPOC domain

pfam15984
Location:2641 → 2722

Collagen_mid; Bacterial collagen, middle region
XM_036164268.1 → XP_036020161.1 msx2-interacting protein isoform X6

UniProtKB/Swiss-Prot

Q62504, Q80TN9, Q99PS4, Q9QZW2

Conserved Domains (6) summary

PTZ00121
Location:213 → 844

PTZ00121; MAEBL; Provisional

PHA03247
Location:1201 → 1635

PHA03247; large tegument protein UL36; Provisional

pfam07744
Location:3053 → 3216

SPOC; SPOC domain

pfam15984
Location:2213 → 2291

Collagen_mid; Bacterial collagen, middle region

cd12350
Location:33 → 106

RRM3_SHARP; RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

cd12351
Location:107 → 183

RRM4_SHARP; RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins