RetrogeneDB ID:

retro_pabe_3390

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:25685590..25685875(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA5
Ensembl ID:ENSPPYG00000017956
Aliases:None
Description:NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001125332]


Retrocopy-Parental alignment summary:






>retro_pabe_3390
AAGAGGCTAAGAATATTGTACACAAAGATCCTTGATGTTCTTAAGCAAACCCCTTAAAAAGCAGTATATAGAAAGTATAC
TGAACAGACTGCAAATGAGAAGCTGGCTATGGTTAAAGCAGAACCAGATGTTAAAAAATTAGAACACCAACTTCAAGGTG
TTCAAATAAAAGAGGTGATTCTTCAGGTTGAAAGTGAACTAAGTCTGGCAAGAAAAATGATACAGCGGAAATGATAGGAG
ATGTTCATGGAAGAGCCTCCTGCCAATCAATGGAAATGGCCAATG

ORF - retro_pabe_3390 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.63 %
Parental protein coverage: 81.9 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVKAEPDVKKLEDQLQGGQLEEVILQAEHELNLA
.RLRILYTKILDVL...P..A.YRKYTEQ..NEKLAMVKAEPDVKKLE.QLQG.Q..EVILQ.E.EL.LA
RetrocopyKRLRILYTKILDVLKQTP*KAVYRKYTEQTANEKLAMVKAEPDVKKLEHQLQGVQIKEVILQVESELSLA
ParentalRKMKEWKLWEPLVEEPPADQWKWPI
RKM...K..E...EEPPA.QWKWP.
RetrocopyRKMIQRK**EMFMEEPPANQWKWPM

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 36 .16 RPM
SRP007412_cerebellum 0 .00 RPM 33 .56 RPM
SRP007412_heart 0 .00 RPM 40 .43 RPM
SRP007412_kidney 0 .00 RPM 30 .40 RPM
SRP007412_liver 0 .00 RPM 10 .13 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3390 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3390 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3390 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4248
Pan troglodytes retro_ptro_2888
Gorilla gorilla retro_ggor_2848

Parental genes homology:
Parental genes homology involve 17 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000045122 retrocopies
Bos taurus ENSBTAG000000093345 retrocopies
Canis familiaris ENSCAFG000000251124 retrocopies
Callithrix jacchus ENSCJAG000000174491 retrocopy
Felis catus ENSFCAG000000271255 retrocopies
Homo sapiens ENSG0000012860910 retrocopies
Gorilla gorilla ENSGGOG000000229229 retrocopies
Loxodonta africana ENSLAFG000000309711 retrocopy
Monodelphis domestica ENSMODG000000153844 retrocopies
Mustela putorius furoENSMPUG000000068114 retrocopies
Mus musculus ENSMUSG000000230892 retrocopies
Otolemur garnettii ENSOGAG000000331376 retrocopies
Pongo abelii ENSPPYG00000017956 10 retrocopies
Pan troglodytes ENSPTRG0000001963710 retrocopies
Rattus norvegicus ENSRNOG000000056983 retrocopies
Sus scrofa ENSSSCG000000166072 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000274041 retrocopy



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