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Aptx aprataxin [ Rattus norvegicus (Norway rat) ]

Gene ID: 259271, updated on 12-Aug-2018

Summary

Official Symbol
Aptxprovided by RGD
Official Full Name
aprataxinprovided by RGD
Primary source
RGD:628740
See related
Ensembl:ENSRNOG00000006582
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
human homolog may play a role in DNA repair [RGD, Feb 2006]
Expression
Biased expression in Testes (RPKM 74.5), Thymus (RPKM 65.8) and 9 other tissues See more
Orthologs

Genomic context

See Aptx in Genome Data Viewer
Location:
5q22
Exon count:
9
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (56987714..57009481, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 5 NC_005104.3 (61521843..61543083, complement)

Chromosome 5 - NC_005104.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108350956 Neighboring gene similar to ribosomal protein L24 Neighboring gene DnaJ heat shock protein family (Hsp40) member A1 Neighboring gene microRNA 207 Neighboring gene SMU1, DNA replication regulator and spliceosomal factor

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA 5'-adenosine monophosphate hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA 5'-adenosine monophosphate hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
DNA 5'-adenosine monophosphate hydrolase activity ISO
Inferred from Sequence Orthology
more info
 
DNA-3'-diphospho-5'-guanosine diphosphatase IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding ISO
Inferred from Sequence Orthology
more info
 
damaged DNA binding IEA
Inferred from Electronic Annotation
more info
 
damaged DNA binding ISO
Inferred from Sequence Orthology
more info
 
double-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
double-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded RNA binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded RNA binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
mismatched DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
molecular_function ND
No biological Data available
more info
 
phosphoglycolate phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
phosphoglycolate phosphatase activity ISO
Inferred from Sequence Orthology
more info
 
phosphoprotein binding IEA
Inferred from Electronic Annotation
more info
 
phosphoprotein binding ISO
Inferred from Sequence Orthology
more info
 
polynucleotide 3'-phosphatase activity ISO
Inferred from Sequence Orthology
more info
 
protein N-terminus binding IEA
Inferred from Electronic Annotation
more info
 
protein N-terminus binding ISO
Inferred from Sequence Orthology
more info
 
single-strand break-containing DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
DNA ligation IEA
Inferred from Electronic Annotation
more info
 
DNA ligation ISO
Inferred from Sequence Orthology
more info
 
biological_process ND
No biological Data available
more info
 
cellular response to DNA damage stimulus ISO
Inferred from Sequence Orthology
more info
 
dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-strand break repair ISO
Inferred from Sequence Orthology
more info
 
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
regulation of protein stability IEA
Inferred from Electronic Annotation
more info
 
regulation of protein stability ISO
Inferred from Sequence Orthology
more info
 
response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
response to hydrogen peroxide ISO
Inferred from Sequence Orthology
more info
 
single strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
single strand break repair IEA
Inferred from Electronic Annotation
more info
 
single strand break repair ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
chromatin ISO
Inferred from Sequence Orthology
more info
 
nuclear chromatin IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with nuclear chromatin ISO
Inferred from Sequence Orthology
more info
 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleolus ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
aprataxin
Names
FHA-HIT
forkhead-associated domain histidine triad-like protein
NP_683687.1
XP_006238089.1
XP_006238090.1
XP_006238091.1
XP_008761829.1
XP_017448660.1

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_148889.2NP_683687.1  aprataxin

    See identical proteins and their annotated locations for NP_683687.1

    Status: PROVISIONAL

    Source sequence(s)
    BC078716
    UniProtKB/Swiss-Prot
    Q8K4H4
    Related
    ENSRNOP00000046400.4, ENSRNOT00000046463.4
    Conserved Domains (3) summary
    cd00060
    Location:2498
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd01278
    Location:151252
    aprataxin_related; aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are ...
    pfam16278
    Location:271327
    zf-C2HE; C2HE / C2H2 / C2HC zinc-binding finger

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005104.4 Reference Rnor_6.0 Primary Assembly

    Range
    56987714..57009481 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008763607.2XP_008761829.1  aprataxin isoform X3

    See identical proteins and their annotated locations for XP_008761829.1

    Conserved Domains (2) summary
    cd01278
    Location:92193
    aprataxin_related; aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are ...
    pfam16278
    Location:212268
    zf-C2HE; C2HE / C2H2 / C2HC zinc-binding finger
  2. XM_006238028.3XP_006238090.1  aprataxin isoform X2

    See identical proteins and their annotated locations for XP_006238090.1

    UniProtKB/Swiss-Prot
    Q8K4H4
    Conserved Domains (3) summary
    cd00060
    Location:2498
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd01278
    Location:151252
    aprataxin_related; aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are ...
    pfam16278
    Location:271327
    zf-C2HE; C2HE / C2H2 / C2HC zinc-binding finger
  3. XM_006238027.3XP_006238089.1  aprataxin isoform X2

    See identical proteins and their annotated locations for XP_006238089.1

    UniProtKB/Swiss-Prot
    Q8K4H4
    Related
    ENSRNOP00000072443.1, ENSRNOT00000090891.1
    Conserved Domains (3) summary
    cd00060
    Location:2498
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd01278
    Location:151252
    aprataxin_related; aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are ...
    pfam16278
    Location:271327
    zf-C2HE; C2HE / C2H2 / C2HC zinc-binding finger
  4. XM_017593171.1XP_017448660.1  aprataxin isoform X1

    Conserved Domains (3) summary
    cd00060
    Location:38112
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd01278
    Location:165266
    aprataxin_related; aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are ...
    pfam16278
    Location:285341
    zf-C2HE; C2HE / C2H2 / C2HC zinc-binding finger
  5. XM_006238029.3XP_006238091.1  aprataxin isoform X3

    See identical proteins and their annotated locations for XP_006238091.1

    Conserved Domains (2) summary
    cd01278
    Location:92193
    aprataxin_related; aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are ...
    pfam16278
    Location:212268
    zf-C2HE; C2HE / C2H2 / C2HC zinc-binding finger

Alternate Rn_Celera

Genomic

  1. AC_000073.1 Alternate Rn_Celera

    Range
    54414271..54435214 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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