RetrogeneDB ID:

retro_pabe_3326

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:8:49053328..49053788(-)
Located in intron of:ENSPPYG00000018571
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2N
Ensembl ID:ENSPPYG00000004832
Aliases:None
Description:Ubiquitin-conjugating enzyme E2 N [Source:UniProtKB/Swiss-Prot;Acc:Q5R7J6]


Retrocopy-Parental alignment summary:






>retro_pabe_3326
ATGGCGGGGCTGCCCTGCAGGATCATCAAGGAAACCCAGCGTTTGCTGGCAGAACCAGTTCCTGGCATCAAAGCAGAACC
AGATGAGAGCAACGCCTGTTATTTTCACGTGGTCATTGCTGGCCCTCAGGATTCCTTCCCCCTTTGAGGGAGGGACTTTT
AAACTTGAACTATTCCTTCCAGAAGAATACTCAATGGCAGCCCCTAAAGTACGTTTCATGACCAAAATTTATCATCCTAG
TGTAGACAAGTTGGGAAGAATATGTTTAGATATTTTGAAAGATAAGTGGTCCCCAGCACTGCAGATCCGCACAGTTCTGC
TATCGATCCAGGCCTTGTTATGCGCTCCCAATCCAGATGATCCATTAGCAAATGATGTAGCGGAGCAGTGGAACACCAAC
AAAGCCCAAGCCATAGAAACAGCTAGAGCATGAACTAGGCTATATGCCATGAATAATATT

ORF - retro_pabe_3326 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.21 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDS-PFEG-GTFKLELFLPEEYPMAAPK
MAGLP.RIIKETQRLLAEPVPGIKAEPDESNA.YFHVVIAGPQDS.P..G.GTFKLELFLPEEY.MAAPK
RetrocopyMAGLPCRIIKETQRLLAEPVPGIKAEPDESNACYFHVVIAGPQDSFPL*G>GTFKLELFLPEEYSMAAPK
ParentalVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIE
VRFMTKIYHP.VDKLGRICLDILKDKWSPALQIRTVLLSIQALL.APNPDDPLANDVAEQW.TN.AQAIE
RetrocopyVRFMTKIYHPSVDKLGRICLDILKDKWSPALQIRTVLLSIQALLCAPNPDDPLANDVAEQWNTNKAQAIE
ParentalTARAWTRLYAMNNI
TARA.TRLYAMNNI
RetrocopyTARA*TRLYAMNNI

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 .11 RPM 88 .24 RPM
SRP007412_cerebellum 0 .00 RPM 90 .59 RPM
SRP007412_heart 0 .12 RPM 27 .97 RPM
SRP007412_kidney 0 .07 RPM 41 .90 RPM
SRP007412_liver 0 .03 RPM 28 .64 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3326 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3326 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3326 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2720

Parental genes homology:
Parental genes homology involve 27 parental genes, and 104 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098331 retrocopy
Bos taurus ENSBTAG000000217672 retrocopies
Canis familiaris ENSCAFG000000061771 retrocopy
Callithrix jacchus ENSCJAG000000029798 retrocopies
Cavia porcellus ENSCPOG000000085815 retrocopies
Dasypus novemcinctus ENSDNOG000000189529 retrocopies
Echinops telfairi ENSETEG000000018825 retrocopies
Felis catus ENSFCAG000000042602 retrocopies
Homo sapiens ENSG000001778893 retrocopies
Loxodonta africana ENSLAFG000000289851 retrocopy
Macropus eugenii ENSMEUG000000029447 retrocopies
Microcebus murinus ENSMICG000000140814 retrocopies
Myotis lucifugus ENSMLUG000000099822 retrocopies
Macaca mulatta ENSMMUG000000206343 retrocopies
Monodelphis domestica ENSMODG000000094512 retrocopies
Mus musculus ENSMUSG000000747816 retrocopies
Nomascus leucogenys ENSNLEG000000056952 retrocopies
Oryctolagus cuniculus ENSOCUG000000112871 retrocopy
Otolemur garnettii ENSOGAG000000344617 retrocopies
Pongo abelii ENSPPYG00000004832 4 retrocopies
Pan troglodytes ENSPTRG000000052973 retrocopies
Sorex araneus ENSSARG000000059453 retrocopies
Sarcophilus harrisii ENSSHAG000000077761 retrocopy
Sus scrofa ENSSSCG000000009084 retrocopies
Tupaia belangeri ENSTBEG0000001249710 retrocopies
Tarsius syrichta ENSTSYG000000088005 retrocopies
Tursiops truncatus ENSTTRG000000033113 retrocopies



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