RetrogeneDB ID:

retro_pabe_1805

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:20:13694489..13694899(-)
Located in intron of:ENSPPYG00000010740
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DUXA
Ensembl ID:ENSPPYG00000010457
Aliases:None
Description:double homeobox A [Source:HGNC Symbol;Acc:32179]


Retrocopy-Parental alignment summary:






>retro_pabe_1805
ATGGCTGAAGACAACTCTTCATACAAGATGGTAGCAACAAGTCATAGGCGCAGTTGCACCAAATTCACAGAAGATTAATT
GAAAATTCTCATCAATAGCTTCAATCAAAAACTTTACTCAGATTATGCTATCAAACAAAAACTTGCTTTAGAAATCAATA
CAGAAGATCCACCCAGAATCCAGATTTGGTTTCAGAATCGAAGAGCTAGGCACAGATTCCAGGAAAGACCAGACCTGAGA
CTTTAGAGTCAAGCCAGAGCCATAAGCAAGATCAACCTGGTAGAGAAGCCAGACGGTGTCGTACTACCTATAGCACCTCT
CAACTATGCACTCTCGACAAGGCATTTATGAAAAACCCATACCCTGGGATTGATTCCAGAGAACAAATTGCTAAATAAAT
TGGTGCTCCA

ORF - retro_pabe_1805 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.13 %
Parental protein coverage: 69.12 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEDTYSHKRVTTNHRRCRTKFTEEQLKILIDTFNQKPYPGYATKQKLALEINTEE-SRIQIWFQNRRAR
MAED..S.K.V.T.HRR..TKFTE..LKILI..FNQK.Y..YA.KQKLALEINTE...RIQIWFQNRRAR
RetrocopyMAEDNSSYKMVATSHRRSCTKFTED*LKILINSFNQKLYSDYAIKQKLALEINTEDPPRIQIWFQNRRAR
ParentalHGFQKRPE-AETLESSQSQGQGQPGVQFQSREARRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEI
H.FQ.RP...ETLESSQS..Q.QPG.....R..R....T...SQL.TL.KAFMKNPYPGIDSRE..AK.I
RetrocopyHRFQERPD<PETLESSQSHKQDQPG--REARRCRTTYST---SQLCTLDKAFMKNPYPGIDSREQIAK*I
ParentalGVP
G.P
RetrocopyGAP

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 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1805 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1805 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1805 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000255051 retrocopy
Felis catus ENSFCAG000000075451 retrocopy
Homo sapiens ENSG000002588735 retrocopies
Gorilla gorilla ENSGGOG000000056507 retrocopies
Loxodonta africana ENSLAFG000000301671 retrocopy
Macaca mulatta ENSMMUG000000077885 retrocopies
Nomascus leucogenys ENSNLEG000000108863 retrocopies
Oryctolagus cuniculus ENSOCUG000000113311 retrocopy
Pongo abelii ENSPPYG00000010457 8 retrocopies
Pan troglodytes ENSPTRG000000288715 retrocopies
Pteropus vampyrus ENSPVAG000000030201 retrocopy
Tupaia belangeri ENSTBEG000000053211 retrocopy
Tarsius syrichta ENSTSYG000000142231 retrocopy
Tursiops truncatus ENSTTRG000000142002 retrocopies



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