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    Sycp1 synaptonemal complex protein 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25276, updated on 27-Nov-2024

    Summary

    Official Symbol
    Sycp1provided by RGD
    Official Full Name
    synaptonemal complex protein 1provided by RGD
    Primary source
    RGD:3794
    See related
    EnsemblRapid:ENSRNOG00000016835 AllianceGenome:RGD:3794
    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
    SCP1
    Summary
    Predicted to enable double-stranded DNA binding activity. Predicted to be involved in meiosis I cell cycle process and protein homotetramerization. Predicted to act upstream of or within regulation of protein localization and sperm DNA condensation. Located in transverse filament. Orthologous to human SYCP1 (synaptonemal complex protein 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward (RPKM 124.1) See more
    Orthologs
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    Genomic context

    See Sycp1 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (192985164..193145234, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (190296688..190456687, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (205274766..205426869, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485942 Neighboring gene tetraspanin 2 Neighboring gene thyroid stimulating hormone subunit beta Neighboring gene nuclear receptor subfamily 1, group H, member 5 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables double-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chiasma assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chiasma assembly IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within chiasma assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in homologous chromosome pairing at meiosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in homologous chromosome pairing at meiosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lateral element assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lateral element assembly IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within lateral element assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in meiotic DNA repair synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in meiotic DNA repair synthesis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within meiotic DNA repair synthesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein homotetramerization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein homotetramerization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein homotetramerization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in reciprocal meiotic recombination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in reciprocal meiotic recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of protein localization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sperm DNA condensation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within sperm DNA condensation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptonemal complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within synaptonemal complex assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptonemal complex assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synaptonemal complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in autosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in autosome ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in central element IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in central element IEA
    Inferred from Electronic Annotation
    more info
     
    located_in central element ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in condensed nuclear chromosome ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in male germ cell nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in male germ cell nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in male germ cell nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in synaptonemal complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptonemal complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synaptonemal complex ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in transverse filament IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in transverse filament IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in transverse filament IEA
    Inferred from Electronic Annotation
    more info
     
    located_in transverse filament ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    synaptonemal complex protein 1
    Names
    A coiled-coil related protein specific for synapsed regions of meiotic prophase chromosomes
    SCP-1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_012810.3NP_036942.2  synaptonemal complex protein 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/Swiss-Prot
      Q03410
      Conserved Domains (1) summary
      pfam05483
      Location:1762
      SCP-1; Synaptonemal complex protein 1 (SCP-1)

    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_086020.1 Reference GRCr8

      Range
      192985164..193145234 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281327.1XP_063137397.1  synaptonemal complex protein 1 isoform X1

      UniProtKB/TrEMBL
      A6K3J6, F1LS76
      Related
      ENSRNOP00000108482.1, ENSRNOT00000131954.1
    2. XM_063281328.1XP_063137398.1  synaptonemal complex protein 1 isoform X2

      Related
      ENSRNOP00000106648.1, ENSRNOT00000163176.1
    3. XM_063281331.1XP_063137401.1  synaptonemal complex protein 1 isoform X3

    4. XM_063281333.1XP_063137403.1  synaptonemal complex protein 1 isoform X5

    5. XM_063281330.1XP_063137400.1  synaptonemal complex protein 1 isoform X2

    6. XM_063281332.1XP_063137402.1  synaptonemal complex protein 1 isoform X4

      Related
      ENSRNOP00000023333.7, ENSRNOT00000023333.7
    7. XM_063281334.1XP_063137404.1  synaptonemal complex protein 1 isoform X6

    8. XM_063281335.1XP_063137405.1  synaptonemal complex protein 1 isoform X7

    9. XM_063281336.1XP_063137406.1  synaptonemal complex protein 1 isoform X8