RetrogeneDB ID:

retro_pabe_3196

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:7_random:2454159..2454447(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TSEN15
Ensembl ID:ENSPPYG00000000421
Aliases:None
Description:tRNA splicing endonuclease 15 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16791]


Retrocopy-Parental alignment summary:






>retro_pabe_3196
GCTCCCTCATGGGCCCTTCAAGGATGGCTGGATGGGCACCCACCCTAAGTGTTTAGAAATGATGGAATGAAGTACAGGAG
ATGACATCCAAGTTTATATAGCATTCTTAGTTTACCTGGACCTCATGGAGAGTAAAAGTTGGCATGAAGTCAATTGTGTG
TGAATGCTGGAACTGCAGCTCATCTGCCTTGTACTGAGCTAGAAGGGGAGGGGCTGCAGACTGTGGTGTCTACCCGCTTC
ACTGCTTCCCTCAGCCATAACTGCTCAAGGGAGATCTTGAAGGCATCT

ORF - retro_pabe_3196 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.74 %
Parental protein coverage: 53.01 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAPSWAPE-DAWMGTHPKYLEMMELDIGDATQVYVAFLVYLDLMESKSWHEVNCVGLPELQLICLVGTEIE
APSWA...D.WMGTHPK.LEMME...GD..QVY.AFLVYLDLMESKSWHEVNCV...ELQLICLV.....
RetrocopyAPSWALQ>DGWMGTHPKCLEMME*STGDDIQVYIAFLVYLDLMESKSWHEVNCV*MLELQLICLV-LS*K
ParentalGEG-LQTVVPTPITASLSHNRIREILKAS
G.G.LQTVV.T..TASLSHN..REILKAS
RetrocopyGRG<LQTVVSTRFTASLSHNCSREILKAS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .00 RPM 0 .83 RPM
SRP007412_cerebellum 0 .00 RPM 1 .09 RPM
SRP007412_heart 0 .00 RPM 0 .81 RPM
SRP007412_kidney 0 .00 RPM 0 .76 RPM
SRP007412_liver 0 .00 RPM 0 .92 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3196 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3196 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3196 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000163691 retrocopy
Callithrix jacchus ENSCJAG000000053561 retrocopy
Dasypus novemcinctus ENSDNOG000000176112 retrocopies
Homo sapiens ENSG000001988601 retrocopy
Gorilla gorilla ENSGGOG000000158042 retrocopies
Loxodonta africana ENSLAFG000000141091 retrocopy
Macaca mulatta ENSMMUG000000164091 retrocopy
Mustela putorius furoENSMPUG000000117901 retrocopy
Mus musculus ENSMUSG000000149801 retrocopy
Nomascus leucogenys ENSNLEG000000180241 retrocopy
Otolemur garnettii ENSOGAG000000031281 retrocopy
Pongo abelii ENSPPYG00000000421 4 retrocopies
Pan troglodytes ENSPTRG000000232022 retrocopies
Pteropus vampyrus ENSPVAG000000011031 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000132302 retrocopies
Vicugna pacos ENSVPAG000000029412 retrocopies



Copyright © RetrogeneDB 2014-2017