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    Specc1 sperm antigen with calponin homology and coiled-coil domains 1 [ Mus musculus (house mouse) ]

    Gene ID: 432572, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Specc1provided by MGI
    Official Full Name
    sperm antigen with calponin homology and coiled-coil domains 1provided by MGI
    Primary source
    MGI:MGI:2442356
    See related
    Ensembl:ENSMUSG00000042331 AllianceGenome:MGI:2442356
    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
    Cytsb; 2810012G08Rik; B230396K10Rik
    Summary
    Acts upstream of or within associative learning and blastocyst development. Located in apical part of cell; cytoplasm; and nucleus. Is expressed in aorta; liver; molar; and ventricular layer. Orthologous to human SPECC1 (sperm antigen with calponin homology and coiled-coil domains 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in cerebellum adult (RPKM 11.0), liver E14.5 (RPKM 7.8) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Specc1 in Genome Data Viewer
    Location:
    11 B2; 11 37.96 cM
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (61847589..62113839)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (61956763..62223013)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 23721 Neighboring gene predicted gene 12273 Neighboring gene endothelial differentiation-related factor 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_29691 Neighboring gene surfeit gene 1 pseudogene Neighboring gene predicted gene, 39988 Neighboring gene STARR-seq mESC enhancer starr_29694 Neighboring gene predicted gene, 39985 Neighboring gene STARR-seq mESC enhancer starr_29695 Neighboring gene STARR-seq mESC enhancer starr_29696 Neighboring gene adenosine A2b receptor Neighboring gene STARR-positive B cell enhancer ABC_E9139 Neighboring gene zinc finger SWIM-type containing 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. m(6)A modification of circSPECC1 suppresses RPE oxidative damage and maintains retinal homeostasis. Chen X, et al. Cell Rep, 2022 Nov 15. PMID 36384115
    2. High-throughput phenotyping of avoidance learning in mice discriminates different genotypes and identifies a novel gene. Maroteaux G, et al. Genes Brain Behav, 2012 Oct. PMID 22846151, Free PMC Article
    3. Genome-wide analysis shows association of epigenetic changes in regulators of Rab and Rho GTPases with spinal muscular atrophy severity. Zheleznyakova GY, et al. Eur J Hum Genet, 2013 Sep. PMID 23299920, Free PMC Article
    4. Expression patterns and biological function of Specc1 during mouse preimplantation development. Lee S, et al. Gene Expr Patterns, 2021 Sep. PMID 34166821
    5. Identification of novel Ack1-interacting proteins and Ack1 phosphorylated sites in mouse brain by mass spectrometry. Del Mar Masdeu M, et al. Oncotarget, 2017 Nov 24. PMID 29254152, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. m[6]A modification of circSPECC1 suppresses RPE oxidative damage and maintains retinal homeostasis.
      Title: m(6)A modification of circSPECC1 suppresses RPE oxidative damage and maintains retinal homeostasis.
    2. Specc1 mutant showes profound and specific delay in avoidance learning.
      Title: High-throughput phenotyping of avoidance learning in mice discriminates different genotypes and identifies a novel gene.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA4061

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within associative learning IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within blastocyst development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in microtubule organizing center IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cytospin-B
    Names
    spectrin domain with coiled-coils 1

    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)

    1. NM_001029936.3 → NP_001025107.1  cytospin-B isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks two 5' coding exons, compared to variant 1. It represents use of an internal promoter and initiates translation at an alternate start codon. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AL592080, AL596110
      Consensus CDS
      CCDS78966.1
      UniProtKB/Swiss-Prot
      Q5DTQ5, Q5SXY0, Q5SXY1, Q8BKR3, Q8BL39
      UniProtKB/TrEMBL
      A0A0J9YUR2
      Related
      ENSMUSP00000144300.2, ENSMUST00000202179.2
      Conserved Domains (3) summary
      cd00014
      Location:876 → 976
      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 ...
      pfam15290
      Location:41 → 218
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp
      cl09111
      Location:556 → 651
      Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

    2. NM_001281818.1 → NP_001268747.1  cytospin-B isoform 1

      See identical proteins and their annotated locations for NP_001268747.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK143663, AL592080, AL596110
      Consensus CDS
      CCDS78965.1
      UniProtKB/Swiss-Prot
      Q5DTQ5, Q5SXY0, Q5SXY1, Q8BKR3, Q8BL39
      UniProtKB/TrEMBL
      A0A0J9YTU3
      Related
      ENSMUSP00000144055.2, ENSMUST00000202389.4
      Conserved Domains (4) summary
      PRK00409
      Location:683 → 783
      PRK00409; recombination and DNA strand exchange inhibitor protein; Reviewed
      TIGR02168
      Location:358 → 726
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam00307
      Location:955 → 1058
      CH; Calponin homology (CH) domain
      pfam09726
      Location:198 → 504
      Macoilin; Macoilin family

    3. NM_001310526.1 → NP_001297455.1  cytospin-B isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK143663, AL592080, BF456202, CB722803, CF532211
      Consensus CDS
      CCDS78964.1
      UniProtKB/TrEMBL
      A0A0J9YUF8, A0A0J9YV86
      Related
      ENSMUSP00000144161.2, ENSMUST00000202178.4
      Conserved Domains (2) summary
      TIGR02168
      Location:358 → 726
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam09726
      Location:198 → 504
      Macoilin; Macoilin 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

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      61847589..62113839
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006533656.4 → XP_006533719.1  cytospin-B isoform X2

      See identical proteins and their annotated locations for XP_006533719.1

      UniProtKB/Swiss-Prot
      Q5DTQ5, Q5SXY0, Q5SXY1, Q8BKR3, Q8BL39
      UniProtKB/TrEMBL
      A0A0J9YTU3
      Related
      ENSMUSP00000143853.2, ENSMUST00000201364.4
      Conserved Domains (4) summary
      PRK00409
      Location:683 → 783
      PRK00409; recombination and DNA strand exchange inhibitor protein; Reviewed
      TIGR02168
      Location:358 → 726
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam00307
      Location:955 → 1058
      CH; Calponin homology (CH) domain
      pfam09726
      Location:198 → 504
      Macoilin; Macoilin family

    2. XM_030246110.2 → XP_030101970.1  cytospin-B isoform X4

      UniProtKB/TrEMBL
      A0A0J9YUF8, A0A0J9YV86
      Related
      ENSMUSP00000063102.8, ENSMUST00000049836.14
      Conserved Domains (2) summary
      TIGR02168
      Location:358 → 726
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam09726
      Location:198 → 504
      Macoilin; Macoilin family

    3. XM_030246108.1 → XP_030101968.1  cytospin-B isoform X1

      UniProtKB/Swiss-Prot
      Q5DTQ5, Q5SXY0, Q5SXY1, Q8BKR3, Q8BL39
      Conserved Domains (5) summary
      PHA03307
      Location:36 → 151
      PHA03307; transcriptional regulator ICP4; Provisional
      COG1196
      Location:165 → 533
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK00409
      Location:697 → 797
      PRK00409; recombination and DNA strand exchange inhibitor protein; Reviewed
      TIGR02168
      Location:372 → 740
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam00307
      Location:969 → 1072
      CH; Calponin homology (CH) domain

    4. XM_030246109.1 → XP_030101969.1  cytospin-B isoform X3

      UniProtKB/TrEMBL
      A0A0J9YV86
      Conserved Domains (3) summary
      PHA03307
      Location:36 → 151
      PHA03307; transcriptional regulator ICP4; Provisional
      TIGR02168
      Location:372 → 740
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam09726
      Location:212 → 518
      Macoilin; Macoilin family

    5. XM_017314640.2 → XP_017170129.1  cytospin-B isoform X5

      UniProtKB/TrEMBL
      A0A0J9YV86
      Related
      ENSMUSP00000144542.2, ENSMUST00000201723.4
      Conserved Domains (3) summary
      TIGR02168
      Location:278 → 646
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR04211
      Location:83 → 179
      SH3_and_anchor; SH3 domain protein
      cl15483
      Location:201 → 347
      Hid1; High-temperature-induced dauer-formation protein

    6. XM_036156821.1 → XP_036012714.1  cytospin-B isoform X6

      UniProtKB/TrEMBL
      A0A0J9YUG8
      Related
      ENSMUSP00000144174.2, ENSMUST00000201015.4
      Conserved Domains (2) summary
      COG1196
      Location:15 → 168
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl00030
      Location:325 → 436
      CH_SF; calponin homology (CH) domain superfamily
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SXY1.2 GenPept UniProtKB/Swiss-Prot:Q5SXY1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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