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    Specc1 sperm antigen with calponin homology and coiled-coil domains 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303208, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Specc1provided by RGD
    Official Full Name
    sperm antigen with calponin homology and coiled-coil domains 1provided by RGD
    Primary source
    RGD:1309718
    See related
    EnsemblRapid:ENSRNOG00000002903 AllianceGenome:RGD:1309718
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Cytsb; RGD1309718
    Summary
    Predicted to be involved in actin cytoskeleton organization. Predicted to act upstream of or within associative learning and blastocyst development. Predicted to be located in apical part of cell; cytosol; and nuclear lumen. Predicted to be part of filamentous actin. Predicted to be active in microtubule organizing center. Orthologous to human SPECC1 (sperm antigen with calponin homology and coiled-coil domains 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 105.7), Spleen (RPKM 69.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Specc1 in Genome Data Viewer
    Location:
    10q22-q23
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (47138351..47412311)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (46638947..46912989)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (48240291..48542171)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene unc-51 like autophagy activating kinase 2 Neighboring gene U6 spliceosomal RNA Neighboring gene A-kinase anchoring protein 10 Neighboring gene uncharacterized LOC134480803 Neighboring gene uncharacterized LOC134480804 Neighboring gene U2 spliceosomal RNA Neighboring gene selenoprotein W, pseudogene 1 Neighboring gene adenosine A2B receptor Neighboring gene zinc finger, SWIM-type containing 7 Neighboring gene tetratricopeptide repeat domain 19

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC116245

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within blastocyst development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in apical part of cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    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
    		  
    is_active_in microtubule organizing center IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cytospin-B

    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_001039017.2 → NP_001034106.1  cytospin-B isoform 1

      See identical proteins and their annotated locations for NP_001034106.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A6HF92, Q4KLM7
      Related
      ENSRNOP00000054612.2, ENSRNOT00000057798.4
      Conserved Domains (1) summary
      cl09111
      Location:636 → 731
      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_001428980.1 → NP_001415909.1  cytospin-B isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      47138351..47412311
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269013.1 → XP_063125083.1  cytospin-B isoform X1

      Related
      ENSRNOP00000073387.3, ENSRNOT00000080682.3

    2. XM_063269014.1 → XP_063125084.1  cytospin-B isoform X3

    3. XM_006246502.5 → XP_006246564.2  cytospin-B isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5D7
      Conserved Domains (2) summary
      TIGR04523
      Location:363 → 782
      Mplasa_alph_rch; helix-rich Mycoplasma protein
      cd21257
      Location:946 → 1057
      CH_CYTSB; calponin homology (CH) domain found in cytospin-B

    4. XM_006246503.5 → XP_006246565.2  cytospin-B isoform X2

      UniProtKB/TrEMBL
      A0A0G2K5D7
      Related
      ENSRNOP00000107244.1, ENSRNOT00000168249.1
      Conserved Domains (3) summary
      PRK00409
      Location:603 → 703
      PRK00409; recombination and DNA strand exchange inhibitor protein; Reviewed
      TIGR02168
      Location:278 → 646
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd21257
      Location:866 → 977
      CH_CYTSB; calponin homology (CH) domain found in cytospin-B

    5. XM_039085967.2 → XP_038941895.1  cytospin-B isoform X4

      Conserved Domains (1) summary
      TIGR02168
      Location:278 → 646
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    6. XM_039085968.2 → XP_038941896.1  cytospin-B isoform X5

      Conserved Domains (2) summary
      COG1196
      Location:58 → 211
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl00030
      Location:368 → 479
      CH_SF; calponin homology (CH) domain superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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