RetrogeneDB ID:

retro_vpac_288

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_387:10108..10840(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS6
Ensembl ID:ENSVPAG00000006030
Aliases:None
Description:ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]


Retrocopy-Parental alignment summary:






>retro_vpac_288
ATGAAGTTGAACATCTCTTTCCGAGGCACTGGTTGCCAGAAACTCACTGAAGTGGATGATAAATGCAAACTTCATACCTT
TTATACAAAGCATATAGCTATAGAAGTTGCTGCTAATGTTCTGGGTGAAGAAATGGAAGGGTTGTATAGTCCAAATCAGT
AGCGGGAAATGATAAACAAGGTTTCCCTATGAAGCAGGGTGTCCTGATCCATGGCTGTGTCTGTTTGCTACTGAGTTAAG
GTGAAGTTCTGGTATAGATCAAGGAAAACTGGAGAAAGAAAGTGCAAATTTGTTCAGGGTTGCATTGCGAATGCCAATCT
AAGTGTTCTCAATTTGGTCATCATAAAAAAAGGGACAGAGAGGATATTCCTGGACTCACTGATAGAACTGTGCCTCATCG
CCCTGGGGTCCAAAATAGCTAGAATTCACAAACTTTTCAATCTCTCTAAAGATGATGTCTGCCAGCATGTCATGAGAAAG
CACCTAAACAGAGAGAGTAAGAAACCAAGGACCAAAGCACCCAAGATGCATGCAGTGTTTGTTACTCCACATGTTCTGTA
ATACAAACAACAATCTATTTGCCCTGAAAGAACAGCATGCTAAGAAAAATAAGGAAAGGCTGCAGAATATGCTAAACTTT
TGACCAAGAGAATGAAGGAGGTCAAAGAAAAACACAAGGAACAAACTACCAAGAGACAGAAGCTGTCCTCTCTGAGAGCT
TCTATCTCCAAG

ORF - retro_vpac_288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.05 %
Parental protein coverage: 97.59 %
Number of stop codons detected: 2
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalMKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEE-WKGYVVRISGG-NDKQGFPMKQGVL
MKLNISF..TGCQKL.EVDD..KL.TFY.K..A.EVAA..LGEE.WKG..V.IS.G.NDKQGFPMKQGVL
RetrocopyMKLNISFRGTGCQKLTEVDDKCKLHTFYTKHIAIEVAANVLGEE>WKGCIVQISSG>NDKQGFPMKQGVL
ParentalTHGRVRLLLSKGHSC-YRPRRTGERKRKSVRGCIVDANLSVLNLVIVK-KGEK-DIPGLTDTTVPRR-LG
.HG.V.LLLS.G....YR.R.TGERK.K.V.GCI..ANLSVLNLVI.K.KG...DIPGLTD.TVP.R.LG
RetrocopyIHGCVCLLLS*GEVL>YRSRKTGERKCKFVQGCIANANLSVLNLVIIK>KGQR>DIPGLTDRTVPHR>LG
ParentalPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRL-VTPRVLQHKRRRI-ALKKQRTKKN
.K.A.RI.KLFNLSK.DDV.Q.V.RK.LN.E.KKPRTKAPK.....VTP.VL..K...I.ALK.Q..KKN
RetrocopySKIA-RIHKLFNLSK-DDVCQHVMRKHLNRESKKPRTKAPKMHAVFVTPHVL*YKQQSI>ALKEQHAKKN
ParentalKE-EAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSK
KE..AAEYAKLL.KRMKE.KEK..EQ..KR..LSSLRAS.SK
RetrocopyKE<KAAEYAKLLTKRMKEVKEKHKEQTTKRQKLSSLRASISK

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_288 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_288 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 15 parental genes, and 135 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000176341 retrocopy
Canis familiaris ENSCAFG000000016154 retrocopies
Callithrix jacchus ENSCJAG000000206126 retrocopies
Cavia porcellus ENSCPOG000000037504 retrocopies
Dasypus novemcinctus ENSDNOG000000072411 retrocopy
Loxodonta africana ENSLAFG000000107664 retrocopies
Microcebus murinus ENSMICG0000000726224 retrocopies
Macaca mulatta ENSMMUG000000034121 retrocopy
Monodelphis domestica ENSMODG000000040951 retrocopy
Mus musculus ENSMUSG0000002849545 retrocopies
Ochotona princeps ENSOPRG000000007516 retrocopies
Ochotona princeps ENSOPRG000000122905 retrocopies
Pongo abelii ENSPPYG0000001919315 retrocopies
Rattus norvegicus ENSRNOG000000490258 retrocopies
Vicugna pacos ENSVPAG00000006030 10 retrocopies



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