RetrogeneDB ID:

retro_cpor_767

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_27:13880166..13880470(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFAB1
Ensembl ID:ENSCPOG00000012038
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_767
CTGGCTTAGATACTCAGCACCACTTTGTGTCCCACCAGGACCAACAGAGGCTCGGTAATGCAGCTGGCCTCAGCCTCCGT
ACTCACACAGGTTCCAGGGAGGATTCTACAAGTTGTGCTGCCTATATAGAGACACACCTCCTTTGACAGAGAAAGGAATC
AAGGATAGGGTTCTGCATGTCTTGAAACTTTGTAACAAGATTGACCCAGAAAAGCTCTCAGTAAATTCCCATTTTATGAA
AGACCTTGGCTTAGACAGTTTGGACCAAATTGAGATTGTCATGGCCATGGGGGATGAATTTGGA

ORF - retro_cpor_767 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.12 %
Parental protein coverage: 64.1 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLARTLSTALCAART-QTRLG-AAQLAL-AFAQVPGRIPQ-FCRQYSDAPPLTLEGIKDRVLYVLKLYDKI
LA..LST.LC..RT.Q.RLG.AA.L.L....QVPGRI.Q..C..Y.D.PPLT..GIKDRVL.VLKL..KI
RetrocopyLA*ILSTTLCPTRT<QQRLGNAAGLSL>VLTQVPGRILQ>LCCLYRDTPPLTEKGIKDRVLHVLKLCNKI
ParentalDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFG
DPEKLSVNSHFMKDLGLDSLDQ.EI.MAM.DEFG
RetrocopyDPEKLSVNSHFMKDLGLDSLDQIEIVMAMGDEFG

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
SRP017611_brain 0 .00 RPM 31 .46 RPM
SRP017611_kidney 0 .00 RPM 83 .96 RPM
SRP017611_liver 0 .00 RPM 55 .93 RPM
SRP040447_lung 0 .05 RPM 19 .70 RPM
SRP040447_skeletal_muscle 0 .00 RPM 115 .06 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_767 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_767 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000143041 retrocopy
Canis familiaris ENSCAFG000000176673 retrocopies
Choloepus hoffmanni ENSCHOG000000035582 retrocopies
Callithrix jacchus ENSCJAG000000206162 retrocopies
Cavia porcellus ENSCPOG00000012038 2 retrocopies
retro_cpor_728, retro_cpor_767 ,
Dasypus novemcinctus ENSDNOG000000171225 retrocopies
Felis catus ENSFCAG000000132413 retrocopies
Homo sapiens ENSG000000047791 retrocopy
Gorilla gorilla ENSGGOG000000063201 retrocopy
Loxodonta africana ENSLAFG000000010321 retrocopy
Macropus eugenii ENSMEUG000000126813 retrocopies
Microcebus murinus ENSMICG000000077782 retrocopies
Macaca mulatta ENSMMUG000000205221 retrocopy
Monodelphis domestica ENSMODG000000163521 retrocopy
Mustela putorius furoENSMPUG000000121422 retrocopies
Mus musculus ENSMUSG000000308696 retrocopies
Oryctolagus cuniculus ENSOCUG000000084571 retrocopy
Otolemur garnettii ENSOGAG000000055622 retrocopies
Pongo abelii ENSPPYG000000071921 retrocopy
Pan troglodytes ENSPTRG000000078891 retrocopy
Rattus norvegicus ENSRNOG000000181292 retrocopies
Sus scrofa ENSSSCG000000107951 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000246572 retrocopies
Tursiops truncatus ENSTTRG000000052582 retrocopies



Copyright © RetrogeneDB 2014-2017