RetrogeneDB ID:

retro_vpac_501

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_262:693571..693837(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TXNDC17
Ensembl ID:ENSVPAG00000001554
Aliases:None
Description:thioredoxin domain containing 17 [Source:HGNC Symbol;Acc:28218]


Retrocopy-Parental alignment summary:






>retro_vpac_501
GAGGACCCAGAAGGAAAAGCCGGTACCCCCGCCACACACAGGCAGCACCAATTCTTTGAGAGGGACCGAGGCCTGTCAGG
GGAGGATGTGTGTTCATCTGTTGCCAAGTAGGAGGAAAACCTTATAGGAAAGACCCAAATAATGATTTCAGAAAAAAATG
TGAGAGCAGCCACAGGGCCCACACTATTTAACTACAGAACTCCTTGATGGCTATACAGTCTGGGCATCTTCAGGCCAACC
TCCCGGAGACGGCTCTCCCTGGAGAT

ORF - retro_vpac_501 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.17 %
Parental protein coverage: 72.36 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKDAEGKSWCPDC-VQAEPVVREGLKHVGEGCVFIYCQVGEKPYWKDPNNDFRKK-LKLTAVPTLLKYGTP
.D.EGK...P....QA.P...EG...V..GCVFI.CQVG.KPY.KDPNNDFRKK.......PTL..Y.TP
RetrocopyEDPEGKAGTPAT<TQAAPIL*EGPRPVRGGCVFICCQVGGKPYRKDPNNDFRKK>VRAATGPTLFNYRTP
ParentalHKL-VESECLQANLVEMLFSED
..L...S..LQANL.E.....D
Retrocopy*WL<IQSGHLQANLPETALPGD

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






RNA-Seq - click to see more details

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Vicugna pacos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_vpac_501 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_501 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 27 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070384 retrocopies
retro_amel_1181, retro_amel_1267, retro_amel_148, retro_amel_344,
Callithrix jacchus ENSCJAG000000111504 retrocopies
retro_cjac_2775, retro_cjac_2877, retro_cjac_2887, retro_cjac_3048,
Cavia porcellus ENSCPOG000000028871 retrocopy
retro_cpor_116,
Equus caballus ENSECAG000000250061 retrocopy
retro_ecab_430,
Echinops telfairi ENSETEG000000019051 retrocopy
retro_etel_14,
Felis catus ENSFCAG000000241431 retrocopy
retro_fcat_1128,
Homo sapiens ENSG000001292352 retrocopies
retro_hsap_132, retro_hsap_2218,
Gorilla gorilla ENSGGOG000000030552 retrocopies
retro_ggor_1750, retro_ggor_230,
Macropus eugenii ENSMEUG000000089461 retrocopy
retro_meug_1771,
Microcebus murinus ENSMICG000000066202 retrocopies
retro_mmur_1093, retro_mmur_766,
Macaca mulatta ENSMMUG000000037882 retrocopies
retro_mmul_365, retro_mmul_932,
Mustela putorius furoENSMPUG000000113382 retrocopies
retro_mputfur_518, retro_mputfur_564,
Mus musculus ENSMUSG000000208033 retrocopies
retro_mmus_2817, retro_mmus_2818, retro_mmus_488,
Nomascus leucogenys ENSNLEG000000092302 retrocopies
retro_nleu_2262, retro_nleu_2516,
Oryctolagus cuniculus ENSOCUG000000165571 retrocopy
retro_ocun_297,
Ochotona princeps ENSOPRG000000005092 retrocopies
retro_opri_575, retro_opri_8,
Procavia capensis ENSPCAG000000037491 retrocopy
retro_pcap_180,
Pongo abelii ENSPPYG000000078801 retrocopy
retro_pabe_485,
Pan troglodytes ENSPTRG000000086442 retrocopies
retro_ptro_137, retro_ptro_1683,
Pteropus vampyrus ENSPVAG000000023991 retrocopy
retro_pvam_1187,
Rattus norvegicus ENSRNOG000000140721 retrocopy
retro_rnor_1700,
Sorex araneus ENSSARG000000065011 retrocopy
retro_sara_20,
Ictidomys tridecemlineatus ENSSTOG000000219862 retrocopies
retro_itri_197, retro_itri_574,
Tupaia belangeri ENSTBEG000000005391 retrocopy
retro_tbel_3760,
Tarsius syrichta ENSTSYG000000109962 retrocopies
retro_tsyr_1058, retro_tsyr_982,
Tursiops truncatus ENSTTRG000000120721 retrocopy
retro_ttru_1252,
Vicugna pacos ENSVPAG00000001554 1 retrocopy
retro_vpac_501 ,


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