RetrogeneDB ID:

retro_ptro_1418

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:20:18704119..18704529(-)
Located in intron of:ENSPTRG00000013291
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DUXA
Ensembl ID:ENSPTRG00000028871
Aliases:None
Description:double homeobox A [Source:HGNC Symbol;Acc:32179]


Retrocopy-Parental alignment summary:






>retro_ptro_1418
ATGGCTGAAGACAACTCTTCACACAAGATGGTAGCAACAAGTCATAGGTGCAGTTGCACCAAATTCACAGAAGATTAATT
GAAAATTCTCATCAATAGCTTCAATCAAAAACTTTACTCAGATTATGCTATCAAACAAAAACTTGCTTTAGAAATCAATA
CAGAAGATCCACCCAGAATCCAGATTTGGTTTCAGAATCGAAGAGCTAGGCACAGATTCCAGGAAAGATCAGACCTGAGA
CTTTAGAGTCAAGCCAGAGCCATAAGCAAGATCAACCTGGTAGAGAAGCCAGACGGTGTCGTACTACCTACAGCACCTCT
CAACTACGCACTCTCAACAAGGCATTTATGAAAAACCCATACCCTGGGATTGATTCCAGAGAACAAATTGCTAAATAAAT
TGGTGCTCCA

ORF - retro_ptro_1418 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.23 %
Parental protein coverage: 69.12 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEDTYSHKMVKTNHRRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEE-SRIQIWFQNRRAR
MAED..SHKMV.T.HR...TKFTE..LKILIN.FNQK.Y..YA.KQKLALEINTE...RIQIWFQNRRAR
RetrocopyMAEDNSSHKMVATSHRCSCTKFTED*LKILINSFNQKLYSDYAIKQKLALEINTEDPPRIQIWFQNRRAR
ParentalHGFQKRPE-AETLESSQSQGQDQPGVEFPSREARRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEI
H.FQ.R....ETLESSQS..QDQPG.E...R..R....T...SQL.TL.KAFMKNPYPGIDSRE..AK.I
RetrocopyHRFQERSD<PETLESSQSHKQDQPGRE--ARRCRTTYST---SQLRTLNKAFMKNPYPGIDSREQIAK*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 .05 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .06 RPM 0 .00 RPM
SRP007412_kidney 0 .03 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1418 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1418 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1418 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2454
Gorilla gorilla retro_ggor_1528
Macaca mulatta retro_mmul_636

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 ENSPPYG000000104578 retrocopies
Pan troglodytes ENSPTRG00000028871 5 retrocopies
Pteropus vampyrus ENSPVAG000000030201 retrocopy
Tupaia belangeri ENSTBEG000000053211 retrocopy
Tarsius syrichta ENSTSYG000000142231 retrocopy
Tursiops truncatus ENSTTRG000000142002 retrocopies



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