RetrogeneDB ID:

retro_pabe_2746

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:69827483..69828110(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1B2
Ensembl ID:ENSPPYG00000013107
Aliases:None
Description:eukaryotic translation elongation factor 1 beta 2 [Source:HGNC Symbol;Acc:3208]


Retrocopy-Parental alignment summary:






>retro_pabe_2746
ATGGGTTTCGGAGACCTGAAAAGCCCCGCGGGCCTCCGGGTGCTCAATGATTACCAGGCAGACAAGAGCTACATCGAGGG
GTATGTGCCATCACAAGCAGATGTGGCAGTATTTGAAGCCGTGTCCAGCCCATCACCTGCTGGCTTGTGTCATGCCCTAC
ATTGGTATAATCACGTCAAGTCTTACGAAAAGGAAAAGGCCAGCCTGCCAGGAGTGAAGAAAGCTTTGGGCAAGTATGGT
CCTGCCAATGTGGAAGGCACTACAGGAAGTGGAGGTACAGATAGTAAAGATGATGATGACATTGATCTCTTTGGATCTGA
TGATGAGGAGGAAAGTGAAGAAGCAAAGAGGCTAAGGGAAGAACGTCTTGCACAATATGAATCAAAGTTAGCCAAAAAAC
TCGCACTTGTTGCCAAGTCTTCCATCTTACTAGATGTGAAACCTTGGGATGATGAGACAGATCTGGCAAAATTAGAGGAG
CGCGTCAGAAGCATTCAAGCAGACGGCTTAGTCTGGGGCTCATCTAAACTAGTTCCAGTGGGATACGGAATTAAGAAACT
TCAAATATAGTGTGTAGTTGAAGATGATAAAGTTGGAACAGATATGCTGGAGGAGCAGATCACTGCA

ORF - retro_pabe_2746 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.82 %
Parental protein coverage: 92.89 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSGPPPADLCHALRWYNHIKSYEKEKASLP
MGFGDLKSPAGL.VLNDY.ADKSYIEGYVPSQADVAVFEAVS.P.PA.LCHAL.WYNH.KSYEKEKASLP
RetrocopyMGFGDLKSPAGLRVLNDYQADKSYIEGYVPSQADVAVFEAVSSPSPAGLCHALHWYNHVKSYEKEKASLP
ParentalGVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAKS
GVKKALGKYGPA.VE.TTGSG.TDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESK.AKK.ALVAKS
RetrocopyGVKKALGKYGPANVEGTTGSGGTDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKLAKKLALVAKS
ParentalSILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
SILLDVKPWDDETD.AKLEE.VRSIQADGLVWGSSKLVPVGYGIKKLQI.CVVEDDKVGTDMLEEQITA
RetrocopySILLDVKPWDDETDLAKLEERVRSIQADGLVWGSSKLVPVGYGIKKLQI*CVVEDDKVGTDMLEEQITA

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 .22 RPM 68 .23 RPM
SRP007412_cerebellum 0 .12 RPM 64 .45 RPM
SRP007412_heart 0 .15 RPM 103 .13 RPM
SRP007412_kidney 0 .27 RPM 128 .28 RPM
SRP007412_liver 0 .43 RPM 234 .81 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2746 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2746 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2746 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3332

Parental genes homology:
Parental genes homology involve 29 parental genes, and 106 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000030151 retrocopy
Bos taurus ENSBTAG000000219798 retrocopies
Canis familiaris ENSCAFG000000296351 retrocopy
Choloepus hoffmanni ENSCHOG000000138351 retrocopy
Callithrix jacchus ENSCJAG000000058052 retrocopies
Cavia porcellus ENSCPOG000000144964 retrocopies
Dipodomys ordii ENSDORG000000036692 retrocopies
Felis catus ENSFCAG000000102391 retrocopy
Homo sapiens ENSG000001149429 retrocopies
Gorilla gorilla ENSGGOG000000070022 retrocopies
Macropus eugenii ENSMEUG000000026548 retrocopies
Microcebus murinus ENSMICG000000106073 retrocopies
Myotis lucifugus ENSMLUG000000166028 retrocopies
Macaca mulatta ENSMMUG000000010546 retrocopies
Nomascus leucogenys ENSNLEG000000070988 retrocopies
Oryctolagus cuniculus ENSOCUG000000098484 retrocopies
Otolemur garnettii ENSOGAG000000112293 retrocopies
Oreochromis niloticus ENSONIG000000176301 retrocopy
Ochotona princeps ENSOPRG000000171633 retrocopies
Oryzias latipes ENSORLG000000185331 retrocopy
Procavia capensis ENSPCAG000000133481 retrocopy
Pongo abelii ENSPPYG00000013107 7 retrocopies
Pteropus vampyrus ENSPVAG000000173342 retrocopies
Sorex araneus ENSSARG000000015241 retrocopy
Sarcophilus harrisii ENSSHAG000000178531 retrocopy
Sus scrofa ENSSSCG000000161281 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000054373 retrocopies
Tupaia belangeri ENSTBEG0000000565713 retrocopies
Xiphophorus maculatus ENSXMAG000000060501 retrocopy



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