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    SYCP1 synaptonemal complex protein 1 [ Homo sapiens (human) ]

    Gene ID: 6847, updated on 5-May-2024

    Summary

    Official Symbol
    SYCP1provided by HGNC
    Official Full Name
    synaptonemal complex protein 1provided by HGNC
    Primary source
    HGNC:HGNC:11487
    See related
    Ensembl:ENSG00000198765 MIM:602162; AllianceGenome:HGNC:11487
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CT8; SCP1; SCP-1; HOM-TES-14
    Summary
    Enables double-stranded DNA binding activity. Involved in protein homotetramerization. Predicted to be located in synaptonemal complex. Predicted to be active in central element; male germ cell nucleus; and transverse filament. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward testis (RPKM 18.8) See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SYCP1 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (114854088..114995370)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (114865527..115006795)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (115397484..115537991)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:115322492-115323058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:115323059-115323624 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115332573-115333482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115333483-115334390 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:115337845-115338062 Neighboring gene suppressor of IKBKE 1 Neighboring gene MPRA-validated peak384 silencer Neighboring gene nuclear receptor subfamily 1 group H member 5, pseudogene Neighboring gene uncharacterized LOC105378915 Neighboring gene Sharpr-MPRA regulatory region 5363 Neighboring gene NANOG hESC enhancer GRCh37_chr1:115589292-115589828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:115604953-115605476 Neighboring gene thyroid stimulating hormone subunit beta Neighboring gene uncharacterized LOC124904359 Neighboring gene tetraspanin 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC104417

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 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 meiotic DNA repair synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein homotetramerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    involved_in sperm DNA condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in synaptonemal complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in autosome IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in central element IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in male germ cell nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synaptonemal complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in transverse filament IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    synaptonemal complex protein 1
    Names
    cancer/testis antigen 8
    testicular tissue protein Li 191

    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_001282541.2NP_001269470.1  synaptonemal complex protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001269470.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AA868393, BC026162, BC144019, BI561137
      Consensus CDS
      CCDS879.1
      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Related
      ENSP00000480997.1, ENST00000618516.4
      Conserved Domains (1) summary
      pfam05483
      Location:28792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
    2. NM_001282542.2NP_001269471.1  synaptonemal complex protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AA868393, AK315268
      Consensus CDS
      CCDS72840.1
      UniProtKB/TrEMBL
      A0A087WZC3, B7ZLS9
      Related
      ENSP00000482532.1, ENST00000613524.4
      Conserved Domains (2) summary
      pfam05483
      Location:28767
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:237331
      TMPIT; TMPIT-like protein
    3. NM_003176.4NP_003167.2  synaptonemal complex protein 1 isoform 1

      See identical proteins and their annotated locations for NP_003167.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AA868393, BC126266, BI561137
      Consensus CDS
      CCDS879.1
      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Related
      ENSP00000358535.3, ENST00000369522.8
      Conserved Domains (1) summary
      pfam05483
      Location:28792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)

    RNA

    1. NR_104211.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA868393, BC026162, BC144020

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      114854088..114995370
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002184.2XP_016857673.1  synaptonemal complex protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Conserved Domains (1) summary
      pfam05483
      Location:28792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
    2. XM_005271156.2XP_005271213.1  synaptonemal complex protein 1 isoform X3

      UniProtKB/TrEMBL
      B7ZLS9
      Conserved Domains (2) summary
      pfam05483
      Location:28737
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:182276
      TMPIT; TMPIT-like protein
    3. XM_005271155.5XP_005271212.1  synaptonemal complex protein 1 isoform X2

      UniProtKB/TrEMBL
      B7ZLS9
      Conserved Domains (2) summary
      pfam05483
      Location:28774
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:219313
      TMPIT; TMPIT-like protein
    4. XM_011542037.3XP_011540339.1  synaptonemal complex protein 1 isoform X5

      UniProtKB/TrEMBL
      Q5VXJ5
      Related
      ENSP00000410011.1, ENST00000455987.5
      Conserved Domains (2) summary
      pfam05483
      Location:28774
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:237331
      TMPIT; TMPIT-like protein
    5. XM_011542039.2XP_011540341.1  synaptonemal complex protein 1 isoform X7

      Conserved Domains (2) summary
      pfam05483
      Location:28549
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:237331
      TMPIT; TMPIT-like protein
    6. XM_006710859.2XP_006710922.1  synaptonemal complex protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006710922.1

      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Related
      ENSP00000358531.1, ENST00000369518.1
      Conserved Domains (1) summary
      pfam05483
      Location:28792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
    7. XM_011542038.2XP_011540340.1  synaptonemal complex protein 1 isoform X6

      Conserved Domains (2) summary
      pfam05483
      Location:1581
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:26120
      TMPIT; TMPIT-like protein
    8. XM_017002185.1XP_016857674.1  synaptonemal complex protein 1 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      114865527..115006795
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338486.1XP_054194461.1  synaptonemal complex protein 1 isoform X1

    2. XM_054338488.1XP_054194463.1  synaptonemal complex protein 1 isoform X3

    3. XM_054338487.1XP_054194462.1  synaptonemal complex protein 1 isoform X2

    4. XM_054338490.1XP_054194465.1  synaptonemal complex protein 1 isoform X5

    5. XM_054338492.1XP_054194467.1  synaptonemal complex protein 1 isoform X7

    6. XM_054338485.1XP_054194460.1  synaptonemal complex protein 1 isoform X1

    7. XM_054338491.1XP_054194466.1  synaptonemal complex protein 1 isoform X6

    8. XM_054338489.1XP_054194464.1  synaptonemal complex protein 1 isoform X4