RetrogeneDB ID:

retro_cpor_245

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_11:6751056..6751527(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7
Ensembl ID:ENSCPOG00000004140
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_245
AAGCTGGTATTTGTCATCTGGATCAAGGGTGTCAAAGGTGTGAACCCAAAGGTCCACAAGGTGCTGCTGCTTCTTCGTCT
TTGCCAGCACTTTGATGGTTCTTTGTTAAGTGCAATAAAGCCTCAGTTAGCATGCTGAGAATTGTGGAACCATATATTTA
ATGGGGTACCCAAGCCAGAGGTCAGTAAAAGAGCTAATACACAAGTGTGGCTGTGACAAAATCAATAAGTGAATTGCCTT
GACAGATAATTCACTGATAACTTGATTCTTGGTAAACAGAGCATCATCAGCATGGAGGATCTGATTAATGAGATTTGTAC
TGCTGAAAAACTCTTCAAAGTGGCAAATAGCTTCGTGTCCCCTTCAAATTGTCATTTCCATGACGTGGGATGAAGAAAAA
GATCCATATTTCATGCCAGGTGGAGATGTTGGAAATGGGGAGACCAGACCAACAGGCTTAGAAGGATGAAC

ORF - retro_cpor_245 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.27 %
Parental protein coverage: 77.78 %
Number of stop codons detected: 3
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT-FVKLNKASVNMLRIVEPYIAW-GYPNLKSVNELIY
KL.FVI.I.G..GV.PKV.KVL.LLRL.Q.F.G..FVK.NKASV.MLRIVEPYI.W.GYP...SV.ELI.
RetrocopyKLVFVIWIKGVKGVNPKVHKVLLLLRLCQHFDGS<FVKCNKASVSMLRIVEPYI*W<GYPSQRSVKELIH
ParentalKRGYGKINKKRIALTDNSLIA-RSLGKYGIICMEDLIHEIYTVGKRFKEANNFL-WPFKLSSPRGGMKK-
K.G..KIN.K.IALTDNSLI....LGK..II.MEDLI.EI.T..K.FK.AN.F...PFKLS.P..GMKK.
RetrocopyKCGCDKIN-K*IALTDNSLIT<LILGKQSIISMEDLINEICTAEKLFKVANSFV<VPFKLSFP*RGMKK<
ParentalKTTHFVEGGDAGNRE-DQINRLIRRMN
K...F..GGD.GN.E.DQ.NRL.RRMN
RetrocopyKDPYFMPGGDVGNGE<DQTNRL-RRMN

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 185 .03 RPM
SRP017611_kidney 0 .00 RPM 270 .09 RPM
SRP017611_liver 0 .00 RPM 197 .22 RPM
SRP040447_lung 0 .00 RPM 309 .49 RPM
SRP040447_skeletal_muscle 0 .00 RPM 315 .34 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_245 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_245 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 10 parental genes, and 96 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000004140 18 retrocopies
Cavia porcellus ENSCPOG000000211892 retrocopies
Erinaceus europaeus ENSEEUG000000103073 retrocopies
Echinops telfairi ENSETEG0000000565633 retrocopies
Latimeria chalumnae ENSLACG000000035711 retrocopy
Macropus eugenii ENSMEUG000000163199 retrocopies
Monodelphis domestica ENSMODG000000071364 retrocopies
Mustela putorius furoENSMPUG0000001024015 retrocopies
Nomascus leucogenys ENSNLEG000000266158 retrocopies
Sorex araneus ENSSARG000000010883 retrocopies



Copyright © RetrogeneDB 2014-2017