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

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, Dec 2024]
Expression: Restricted expression toward (RPKM 124.1) See more
Orthologs: human mouse all
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Genomic context

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_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SCP1 has the potential to induce cardiac hypertrophy; however, the effect is suppressed by intronic miR-26b in cardiomyocytes. miR-26b has an antagonistic effect on its host gene SCP1.
Title: MicroRNA 26b encoded by the intron of small CTD phosphatase (SCP) 1 has an antagonistic effect on its host gene.
Premature loss of SCP1 resulted in more oocytes reaching diplotene stage, evidenced by decrease in number of oocytes containing germ cell nuclear antigen-1 and increase in number of oocytes expressing MSY2(expressed in oocytes arrested in diplotene).
Title: Loss of synaptonemal complex protein-1, a synaptonemal complex protein, contributes to the initiation of follicular assembly in the developing rat ovary.
SCP1 is a primary determinant of SC assembly that plays a key role in synapsis of homologous chromosomes
Title: Mammalian protein SCP1 forms synaptonemal complex-like structures in the absence of meiotic chromosomes.

Submit: New GeneRIF Correction

General gene information

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Markers

L18248 (e-PCR)
- UniSTS:25892

Sycp1 (e-PCR), detects polymorphism
- UniSTS:265268

d2rat233 (e-PCR)
- UniSTS:121682

D2Got129 (e-PCR)
- UniSTS:113799

Sycp1 (e-PCR), detects polymorphism
- UniSTS:275903

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

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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)

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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)

NM_012810.3 → NP_036942.2 synaptonemal complex protein 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

Q03410

Conserved Domains (1) summary

pfam05483
Location:1 → 762

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

NC_086020.1 Reference GRCr8

Range

192985164..193145234 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q03410

UniProtKB/TrEMBL

A6K3J6, F1LS76

Related

ENSRNOP00000108482.1, ENSRNOT00000131954.1
XM_063281328.1 → XP_063137398.1 synaptonemal complex protein 1 isoform X2

UniProtKB/Swiss-Prot

Q03410

Related

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

UniProtKB/Swiss-Prot

Q03410
XM_063281333.1 → XP_063137403.1 synaptonemal complex protein 1 isoform X5

UniProtKB/Swiss-Prot

Q03410
XM_063281330.1 → XP_063137400.1 synaptonemal complex protein 1 isoform X2

UniProtKB/Swiss-Prot

Q03410
XM_063281332.1 → XP_063137402.1 synaptonemal complex protein 1 isoform X4

UniProtKB/Swiss-Prot

Q03410

Related

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

UniProtKB/Swiss-Prot

Q03410
XM_063281335.1 → XP_063137405.1 synaptonemal complex protein 1 isoform X7
XM_063281336.1 → XP_063137406.1 synaptonemal complex protein 1 isoform X8