Specc1l sperm antigen with calponin homology and coiled-coil domains 1-like [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Specc1lprovided by MGI
Official Full Name: sperm antigen with calponin homology and coiled-coil domains 1-likeprovided by MGI
Primary source: MGI:MGI:1921642
See related: Ensembl:ENSMUSG00000033444 AllianceGenome:MGI:1921642
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: Cytsa; mKIAA0376; 4930470P14Rik; 4932439K10Rik; 9530057A13Rik
Summary: Enables beta-catenin binding activity. Acts upstream of or within several processes, including anterior neural tube closure; negative regulation of protein depolymerization; and positive regulation of protein kinase B signaling. Located in cell-cell junction; cytoplasm; and cytoskeleton. Part of filamentous actin. Is expressed in 1st branchial arch maxillary component; branchial arch; eye; fronto-nasal process; and limb. Human ortholog(s) of this gene implicated in Opitz GBBB syndrome type II and oblique facial clefting 1. Orthologous to human SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1 like). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in lung adult (RPKM 17.1), large intestine adult (RPKM 10.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 38.51 cM

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (75047872..75148234)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (75212037..75312400)

Chromosome 10 - NC_000076.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics.
Title: SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics.
In-frame deletion of SPECC1L microtubule association domain results in gain-of-function phenotypes affecting embryonic tissue movement and fusion events.
Title: In-frame deletion of SPECC1L microtubule association domain results in gain-of-function phenotypes affecting embryonic tissue movement and fusion events.
SPECC1L-deficient primary mouse embryonic palatal mesenchyme cells show speed and directionality defects.
Title: SPECC1L-deficient primary mouse embryonic palatal mesenchyme cells show speed and directionality defects.
SPECC1L regulates palate development downstream of IRF6.
Title: SPECC1L regulates palate development downstream of IRF6.
SPECC1L as a novel modulator of PI3K-AKT signaling and AJ biology, required for neural tube closure and CNCC delamination.
Title: SPECC1L deficiency results in increased adherens junction stability and reduced cranial neural crest cell delamination.

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Variation

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Alleles

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

Gene trapped (2)
Targeted (1) 1 citation
Endonuclease-mediated (8) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10Mit116 (e-PCR), detects polymorphism
- UniSTS:126014

NoName (e-PCR)
- UniSTS:236379

NoName (e-PCR)
- UniSTS:236380

D10Mit91 (e-PCR), detects polymorphism
- UniSTS:116621

AW553442 (e-PCR)
- UniSTS:208559

D10Mit225 (e-PCR), detects polymorphism
- UniSTS:126128

RH136175 (e-PCR)
- UniSTS:210170

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within actin cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within adherens junction organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell adhesion	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within face morphogenesis	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within negative regulation of actin filament depolymerization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of microtubule depolymerization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neural crest cell delamination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
located_in cell-cell junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
part_of filamentous actin	IDA Inferred from Direct Assay more info	PubMed
located_in gap junction	IEA Inferred from Electronic Annotation more info
located_in microtubule cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
is_active_in microtubule organizing center	IBA Inferred from Biological aspect of Ancestor more info
located_in microtubule organizing center	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cytospin-A

Names: SPECC1-like protein

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_001145826.1 → NP_001139298.1 cytospin-A isoform a

See identical proteins and their annotated locations for NP_001139298.1

Status: VALIDATED

Description

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

Source sequence(s)

AB093236, AI853253, BC072595

Consensus CDS

CCDS48598.1

UniProtKB/TrEMBL

A0A0R4J0J8, Q6GQV8

Related

ENSMUSP00000101061.4, ENSMUST00000105421.10

Conserved Domains (4) summary

COG1196
Location:518 → 819

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd00014
Location:1033 → 1133

CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...

TIGR02168
Location:219 → 843

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam15301
Location:839 → 980

SLAIN; SLAIN motif-containing family
NM_153406.3 → NP_700455.3 cytospin-A isoform b

See identical proteins and their annotated locations for NP_700455.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream translational start codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus, compared to isoform a.

Source sequence(s)

AI853253, AK041543, AY884297, BC072595

Consensus CDS

CCDS48599.1

UniProtKB/Swiss-Prot

Q2KN98, Q8CHF9

UniProtKB/TrEMBL

Q6GQV8

Related

ENSMUSP00000151322.2, ENSMUST00000218766.2

Conserved Domains (3) summary

COG1196
Location:501 → 802

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:202 → 826

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd21199
Location:1006 → 1117

CH_CYTS; calponin homology (CH) domain found in the cytospin family

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_000076.7 Reference GRCm39 C57BL/6J

Range

75047872..75148234

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017314127.2 → XP_017169616.1 cytospin-A isoform X2

UniProtKB/Swiss-Prot

Q2KN98, Q8CHF9

UniProtKB/TrEMBL

Q6GQV8

Conserved Domains (3) summary

COG1196
Location:501 → 802

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:202 → 826

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd21199
Location:1006 → 1117

CH_CYTS; calponin homology (CH) domain found in the cytospin family
XM_030245333.2 → XP_030101193.1 cytospin-A isoform X2

UniProtKB/Swiss-Prot

Q2KN98, Q8CHF9

UniProtKB/TrEMBL

Q6GQV8

Conserved Domains (3) summary

COG1196
Location:501 → 802

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:202 → 826

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd21199
Location:1006 → 1117

CH_CYTS; calponin homology (CH) domain found in the cytospin family
XM_006514252.5 → XP_006514315.1 cytospin-A isoform X2

See identical proteins and their annotated locations for XP_006514315.1

UniProtKB/Swiss-Prot

Q2KN98, Q8CHF9

UniProtKB/TrEMBL

Q6GQV8

Conserved Domains (3) summary

COG1196
Location:501 → 802

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:202 → 826

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd21199
Location:1006 → 1117

CH_CYTS; calponin homology (CH) domain found in the cytospin family
XM_036156062.1 → XP_036011955.1 cytospin-A isoform X2

UniProtKB/Swiss-Prot

Q2KN98, Q8CHF9

UniProtKB/TrEMBL

Q6GQV8

Conserved Domains (3) summary

COG1196
Location:501 → 802

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:202 → 826

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd21199
Location:1006 → 1117

CH_CYTS; calponin homology (CH) domain found in the cytospin family
XM_011243589.3 → XP_011241891.1 cytospin-A isoform X1

See identical proteins and their annotated locations for XP_011241891.1

UniProtKB/TrEMBL

A0A0R4J0J8, Q6GQV8

Related

ENSMUSP00000045099.8, ENSMUST00000040105.8

Conserved Domains (4) summary

COG1196
Location:518 → 819

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd00014
Location:1033 → 1133

CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...

TIGR02168
Location:219 → 843

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam15301
Location:839 → 980

SLAIN; SLAIN motif-containing family