Xab2 XPA binding protein 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Xab2provided by RGD
Official Full Name: XPA binding protein 2provided by RGD
Primary source: RGD:621217
See related: EnsemblRapid:ENSRNOG00000000988 AllianceGenome:RGD:621217
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
Also known as: Ath55
Summary: Involved in cerebral cortex development. Predicted to be located in nucleoplasm. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Orthologous to human XAB2 (XPA binding protein 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 124.4), Spleen (RPKM 108.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 12p12

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (6465569..6477616, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (1667672..1679702, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (2158391..2170397, complement)

Chromosome 12 - NC_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

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General gene information

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Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in blastocyst development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within blastocyst development	ISO Inferred from Sequence Orthology more info
involved_in cerebral cortex development	IEP Inferred from Expression Pattern more info	PubMed
involved_in generation of catalytic spliceosome for first transesterification step	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in transcription-coupled nucleotide-excision repair	IEA Inferred from Electronic Annotation more info
involved_in transcription-coupled nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in transcription-coupled nucleotide-excision repair	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
part_of Prp19 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type catalytic step 2 spliceosome	IEA Inferred from Electronic Annotation more info
part_of U2-type catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
part_of U2-type catalytic step 2 spliceosome	ISS Inferred from Sequence or Structural Similarity more info
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of post-mRNA release spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: pre-mRNA-splicing factor SYF1

Names: adapter protein ATH-55

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_139109.2 → NP_620809.1 pre-mRNA-splicing factor SYF1

See identical proteins and their annotated locations for NP_620809.1

Status: PROVISIONAL

Source sequence(s)

AF277899

UniProtKB/Swiss-Prot

Q99PK0

UniProtKB/TrEMBL

A0A8L2PZV6, A6KQ13

Related

ENSRNOP00000001309.4, ENSRNOT00000001309.6

Conserved Domains (2) summary

COG0457
Location:272 → 549

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:389 → 424

TPR; TPR repeat [structural motif]

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_086030.1 Reference GRCr8

Range

6465569..6477616 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089058.2 → XP_038944986.1 pre-mRNA-splicing factor SYF1 isoform X1

UniProtKB/TrEMBL

A0A8I5XWU2, A6KQ14

Conserved Domains (2) summary

COG0457
Location:167 → 444

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:284 → 319

TPR; TPR repeat [structural motif]