RetrogeneDB ID:

retro_vpac_88

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_1646:1132187..1132613(+)
Located in intron of:ENSVPAG00000009173
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSVPAG00000004235
Aliases:None
Description:ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]


Retrocopy-Parental alignment summary:






>retro_vpac_88
CATGTTGCTGTCAAGGCTACTGACGGTCATTTGCTTTTTCTGTTCTGTGTTGGTTTTACTAAAAAAACAAAATGCAGCAA
TCAGACTGAGAAGACTTCTGATGCGCAGCACCAGCAAGTCCACCAAATCTCAACAAAAATGGAAATCATGACCCGAAAGG
TGCAGACAAATGATTTGAAATAATCGGTCAACAAAATGATTCCAGATAGCATTGGAAAAGATATAGAAAAGACTTGCTAA
TCTATTTATTCCCTCCACGACGTAGTCATTAGAAAGGTAAAAATAATAAAGAAGCCTCATCTGAATTGGGAAAACTCAAA
TGAATTTCATGGGGAAGGTAGTCGTTCTGGAAAAGCTACTGGGGATGAGGTAGGTGTTAAAGTTGAGCAAGCTGAAGGAT
ATGAGTCCTCAGTCCAAGAATCGCTT

ORF - retro_vpac_88 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.41 %
Parental protein coverage: 53.41 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalHVDVKTTDGYLLRLFCVGFTKKR--NNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPD
HV.VK.TDG.LL.LFCVGFTKK....NQ..KTS.AQHQQV.QI..KM.EIMTR.VQTNDLK..VNK.IPD
RetrocopyHVAVKATDGHLLFLFCVGFTKKTKCSNQTEKTSDAQHQQVHQISTKM-EIMTRKVQTNDLK*SVNKMIPD
ParentalSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKF-ELGKLM-ELHGEGSSSGKATGDETGAKVERADGYEPP
SIGKDIEK.C.SIY.LHDV..RKVK..KKP...ELGKL..E.HGEGS.SGKATGDE.G.KVE.A.GYE..
RetrocopySIGKDIEKTC*SIYSLHDVVIRKVKIIKKPHL<ELGKLK>EFHGEGSRSGKATGDEVGVKVEQAEGYESS
ParentalVQESV
VQES.
RetrocopyVQESL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Vicugna pacos was not studied using RNA-Seq expression data.
Vicugna pacos was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_vpac_88 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_88 was not experimentally validated.

Retrocopy orthology:
Vicugna pacos 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 13 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001842511 retrocopies
Bos taurus ENSBTAG000000099083 retrocopies
Canis familiaris ENSCAFG000000079907 retrocopies
Callithrix jacchus ENSCJAG000000022687 retrocopies
Gorilla gorilla ENSGGOG000000031822 retrocopies
Microcebus murinus ENSMICG000000049219 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Vicugna pacos ENSVPAG00000004235 8 retrocopies



Copyright © RetrogeneDB 2014-2017