RetrogeneDB ID:

retro_pabe_845

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:52906772..52907167(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VTI1B
Ensembl ID:ENSPPYG00000005927
Aliases:None
Description:vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]


Retrocopy-Parental alignment summary:






>retro_pabe_845
GAGCATTTTGAGCAGCTGCATGAGATGTGCCTCCAAGGGGTGCACTAGTGGCTGCTGGGTATGGCAGGGACCCAGGAGAA
GTTGATCAGAGATTTTGATGAAAAGCAACAGGAAGCAAACAAAATGCTGGCACAGATGGAGGAGGAACTACATTATGCAC
CCCTATCTTTCCATAACCCCATGATGTCTAAGCTTCGAGACTATCAGAAGGACCTTGCCCAACTCCATCTGGAGGCAAGA
AGTACACCTTTGCAGCCATGCCTAGGGACCGAGGAGACATGAAATATGGCACATATGCTGTAGAGAATGAGCATGTGAAT
AGGCTACAGTCTCAAAGGGCAATGCTTCTCCAAGGCACCAAAATCCTGGGCCGGGCCACCCAAGAGACTGACCAG

ORF - retro_pabe_845 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.33 %
Parental protein coverage: 57.33 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEIFRGLHED-LQGVPERLLGTAGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAPLSFRNPMMSKLRNY
E.F..LHE..LQGV...LLG.AGT.E..KLIRDFDEKQQEAN..LA.MEEEL.YAPLSF.NPMMSKLR.Y
RetrocopyEHFEQLHEMCLQGVH*WLLGMAGTQE--KLIRDFDEKQQEANKMLAQMEEELHYAPLSFHNPMMSKLRDY
ParentalRKDLAKLHREVRSTPL-TATPGGRGDMKYGIYAVENEHMNRLQSQRAMLLQGTESLNRATQSIER
.KDLA.LH.E.RSTPL..A.P..RGDMKYG.YAVENEH.NRLQSQRAMLLQGT..L.RATQ....
RetrocopyQKDLAQLHLEARSTPL<AAMPRDRGDMKYGTYAVENEHVNRLQSQRAMLLQGTKILGRATQETDQ

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 80 .61 RPM
SRP007412_cerebellum 0 .00 RPM 47 .42 RPM
SRP007412_heart 0 .00 RPM 29 .11 RPM
SRP007412_kidney 0 .00 RPM 83 .36 RPM
SRP007412_liver 0 .00 RPM 40 .30 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_845 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_845 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_845 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152631 retrocopy
Dasypus novemcinctus ENSDNOG000000036432 retrocopies
Dipodomys ordii ENSDORG000000159392 retrocopies
Echinops telfairi ENSETEG000000061011 retrocopy
Felis catus ENSFCAG000000140901 retrocopy
Homo sapiens ENSG000001005683 retrocopies
Gorilla gorilla ENSGGOG000000056202 retrocopies
Macropus eugenii ENSMEUG000000049102 retrocopies
Microcebus murinus ENSMICG000000108431 retrocopy
Myotis lucifugus ENSMLUG000000111843 retrocopies
Macaca mulatta ENSMMUG000000158661 retrocopy
Mustela putorius furoENSMPUG000000071301 retrocopy
Nomascus leucogenys ENSNLEG000000007804 retrocopies
Pongo abelii ENSPPYG00000005927 5 retrocopies
Pan troglodytes ENSPTRG000000064683 retrocopies
Pteropus vampyrus ENSPVAG000000116713 retrocopies
Tupaia belangeri ENSTBEG000000030491 retrocopy
Tarsius syrichta ENSTSYG000000076882 retrocopies



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