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

Gene ID: 6847, updated on 17-Jun-2019

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
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
Expression
Restricted expression toward testis (RPKM 18.8) See more
Orthologs

Genomic context

See SYCP1 in Genome Data Viewer
Location:
1p13.2
Exon count:
38
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (114854268..114995370)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (115397455..115537991)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene suppressor of IKBKE 1 Neighboring gene nuclear receptor subfamily 1 group H member 5, pseudogene Neighboring gene uncharacterized LOC105378915 Neighboring gene thyroid stimulating hormone subunit beta 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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Meiosis, organism-specific biosystem (from REACTOME)
    Meiosis, organism-specific biosystemDuring meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing...
  • Meiotic synapsis, organism-specific biosystem (from REACTOME)
    Meiotic synapsis, organism-specific biosystemMeiotic synapsis is the stable physical pairing of homologous chromosomes that begins in leptonema of prophase I and lasts until anaphase of prophase I. First, short segments of axial elements form a...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC104417

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding TAS
Traceable Author Statement
more info
PubMed 
double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cell division IEA
Inferred from Electronic Annotation
more info
 
chiasma assembly IEA
Inferred from Electronic Annotation
more info
 
lateral element assembly IEA
Inferred from Electronic Annotation
more info
 
meiotic DNA repair synthesis IEA
Inferred from Electronic Annotation
more info
 
protein homotetramerization IDA
Inferred from Direct Assay
more info
PubMed 
reciprocal meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein localization IEA
Inferred from Electronic Annotation
more info
 
sperm chromatin condensation IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis TAS
Traceable Author Statement
more info
PubMed 
synapsis ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptonemal complex assembly ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Component Evidence Code Pubs
central element IEA
Inferred from Electronic Annotation
more info
 
chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
male germ cell nucleus IEA
Inferred from Electronic Annotation
more info
 
synaptonemal complex ISS
Inferred from Sequence or Structural Similarity
more info
 
transverse filament IEA
Inferred from Electronic Annotation
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)

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_001282541.1NP_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
    Q15431
    UniProtKB/TrEMBL
    A0A024R0I2, B7ZLS9
    Related
    ENSP00000480997.1, ENST00000618516.4
    Conserved Domains (1) summary
    pfam05483
    Location:28792
    SCP-1; Synaptonemal complex protein 1 (SCP-1)
  2. NM_001282542.1NP_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, BI561137
    Consensus CDS
    CCDS72840.1
    UniProtKB/TrEMBL
    A0A087WZC3
    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
    Q15431
    UniProtKB/TrEMBL
    A0A024R0I2
    Related
    ENSP00000358535.3, ENST00000369522.8
    Conserved Domains (1) summary
    pfam05483
    Location:28792
    SCP-1; Synaptonemal complex protein 1 (SCP-1)

RNA

  1. NR_104211.1 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, BI561137

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    114854268..114995370
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    Q15431
    UniProtKB/TrEMBL
    A0A024R0I2
    Conserved Domains (1) summary
    pfam05483
    Location:28792
    SCP-1; Synaptonemal complex protein 1 (SCP-1)
  2. XM_005271155.4XP_005271212.1  synaptonemal complex protein 1 isoform X2

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

    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
  4. XM_011542039.1XP_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
  5. XM_005271156.1XP_005271213.1  synaptonemal complex protein 1 isoform X3

    Conserved Domains (2) summary
    pfam05483
    Location:28737
    SCP-1; Synaptonemal complex protein 1 (SCP-1)
    pfam07851
    Location:182276
    TMPIT; TMPIT-like protein
  6. XM_006710859.1XP_006710922.1  synaptonemal complex protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006710922.1

    UniProtKB/Swiss-Prot
    Q15431
    UniProtKB/TrEMBL
    A0A024R0I2
    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

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