Sycp2 synaptonemal complex protein 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sycp2provided by RGD
Official Full Name: synaptonemal complex protein 2provided by RGD
Primary source: RGD:69429
See related: EnsemblRapid:ENSRNOG00000061690 AllianceGenome:RGD:69429
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA binding activity. Predicted to be involved in meiotic recombination checkpoint signaling and synaptonemal complex assembly. Predicted to act upstream of or within several processes, including male genitalia morphogenesis; meiotic nuclear division; and negative regulation of apoptotic process. Located in lateral element. Human ortholog(s) of this gene implicated in spermatogenic failure 1. Orthologous to human SYCP2 (synaptonemal complex protein 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Testes (RPKM 180.0) and Heart (RPKM 10.3) See more
Orthologs: human mouse all
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Genomic context

Location:: 3q43

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (185814033..185876516, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (165431715..165502134, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (173884559..173948304, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

Using the yeast two-hybrid system, the C-terminus of SYCP1 directly interacts with SYCP2.
Title: Protein SYCP2 provides a link between transverse filaments and lateral elements of mammalian synaptonemal complexes.

Submit: New GeneRIF Correction

General gene information

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Markers

G65197 (e-PCR)
- UniSTS:225878

D3Got171 (e-PCR)
- UniSTS:113382

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in ectopic germ cell programmed cell death	IEA Inferred from Electronic Annotation more info
acts_upstream_of ectopic germ cell programmed cell death	ISO Inferred from Sequence Orthology more info
involved_in female meiotic nuclear division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within female meiotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in fertilization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within fertilization	ISO Inferred from Sequence Orthology more info
involved_in male genitalia morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within male genitalia morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in male meiotic nuclear division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within male meiotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in meiotic recombination checkpoint signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of developmental process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of developmental process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of reproductive process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of reproductive process	ISO Inferred from Sequence Orthology more info
involved_in synaptonemal complex assembly	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
is_active_in condensed chromosome, centromeric region	IBA Inferred from Biological aspect of Ancestor more info
is_active_in lateral element	IBA Inferred from Biological aspect of Ancestor more info
located_in lateral element	IDA Inferred from Direct Assay more info	PubMed
located_in lateral element	IEA Inferred from Electronic Annotation more info
located_in lateral element	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in synaptonemal complex	IDA Inferred from Direct Assay more info	PubMed
located_in synaptonemal complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: synaptonemal complex protein 2

Names: SCP-2; rnSCP2; synaptonemal complex lateral element protein

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_130735.1 → NP_570091.1 synaptonemal complex protein 2

See identical proteins and their annotated locations for NP_570091.1

Status: PROVISIONAL

Source sequence(s)

Y08981

UniProtKB/Swiss-Prot

O70608

UniProtKB/TrEMBL

A0A8L2R2I5

Related

ENSRNOP00000075596.3, ENSRNOT00000079019.3

Conserved Domains (2) summary

pfam18581
Location:10 → 184

SYCP2_ARLD; Synaptonemal complex 2 armadillo-repeat-like domain

pfam18584
Location:278 → 389

SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain

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_086021.1 Reference GRCr8

Range

185814033..185876516 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063284681.1 → XP_063140751.1 synaptonemal complex protein 2 isoform X2
XM_063284684.1 → XP_063140754.1 synaptonemal complex protein 2 isoform X3

Related

ENSRNOP00000107503.1, ENSRNOT00000153265.1
XM_063284678.1 → XP_063140748.1 synaptonemal complex protein 2 isoform X1

UniProtKB/Swiss-Prot

O70608
XM_063284679.1 → XP_063140749.1 synaptonemal complex protein 2 isoform X1

UniProtKB/Swiss-Prot

O70608
XM_063284682.1 → XP_063140752.1 synaptonemal complex protein 2 isoform X2
XM_063284680.1 → XP_063140750.1 synaptonemal complex protein 2 isoform X1

UniProtKB/Swiss-Prot

O70608
XM_063284683.1 → XP_063140753.1 synaptonemal complex protein 2 isoform X2
XM_039105970.2 → XP_038961898.1 synaptonemal complex protein 2 isoform X4

UniProtKB/TrEMBL

A0A8L2RBT5

Conserved Domains (1) summary

pfam18584
Location:53 → 164

SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain