RetrogeneDB ID:

retro_vpac_100

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_182:261108..261934(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL6
Ensembl ID:ENSVPAG00000007000
Aliases:None
Description:ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]


Retrocopy-Parental alignment summary:






>retro_vpac_100
CAGAAGAAACCTGAAGCCAAGAAGGCTGATGCCAGGGCAAGGTCCAGAAGAGAAACCTCAAGACCAAAGCACCTCAGAAG
GGGAAACCTCACCACAACCAAAGCCCCATCCTAGTCAGAGGAATTGGCAGCTTTTCCCCACCTGCTGTGTGTTCCAGCAA
GGCCATGTACAAGAAGAAGTAGTCAGCACCTATATTTAAGGTTGCAAAGAAAAAGAAGGAGAAATCTCTTGCTGCTGACA
CCAAACCAGTTGGTGGTGACAGAGGTGGTGAGACCCAGGCGATCATGCTCTGCAGGACGCCTGCAGACTCTTCTACTGAA
GGTGTGCCGTGGAAGCTCTTGGGCCGTAGGAGAAAGCCCTTCTGTCAGATGTGAGGAAGCTGCCAGCTGGCATCACTCCC
AGAGCCACTCCGAGCATCCTCACTGGGTGCTGCAGAGGCTAAACGGTGGTTTTCCTGAAGCAGCTGGGCAGAAGCTTGCT
GCTTGTGACTGGACCTCTCATCCTCAGTCGAGTTCCTCTGCTGAAACACACCAGAAATTTGTCATCACCACCTCCACCAA
AATGGATATGAGTGGTGTGGAAATCCCAGAACATCTCCCTGAGGCTTACTTCAGGAAGAAGCAGCTTGGGAAAGCCCAGA
TACCAGGAAGGTGAGCACTTCGACACAGGGACAGGGAAATCTGAGCCCACAGAGCAGCACAGGGTCAATCCGAGAGCTGT
GGGCTCCAATGCTGCCGAAAACTCACAGCCGTTCCTCAGCTCCAGGGTGACCTCTGTTCTGAACTTTTCTCTCACAAATG
AAATTTATCCTCACAGATTGGTGTTC

ORF - retro_vpac_100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.16 %
Parental protein coverage: 95.83 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalEKKPEAKKADAG-GKVKKADGKVKKAKKGRPHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYSAAKSKVE
.KKPEAKKADA..GKV.K...K.K...KG.PH....P.LVRGIG..S..A..S.KA.YK.K.SA...KV.
RetrocopyQKKPEAKKADAR<GKVQKRNLKTKAPQKGKPHHNQSPILVRGIGSFSPPAVCSSKAMYKKK*SAPIFKVA
ParentalKKKKVRVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSK-HVRKLRASITPGTIL
KKKK...LA..TKPVGGD..G.T....L...P....TE.VP.KLL....KPF....VRKL.A.ITP....
RetrocopyKKKKEKSLAADTKPVGGDRGGETQAIMLCRTPADSSTEGVPWKLLGRRRKPFCQ<DVRKLPAGITPRATP
ParentalIILTGRHRGKRVIFLKQLSSGLLLVTGPLSLNRVPLRR-THQKFVIATSTKIDISGVKIPEHLTDTYFKK
.ILTG..RG..V.FLKQL...LLLVTGPL.L.RVPL...THQKFVI.TSTK.D.SGV.IPEHL...YF.K
RetrocopySILTGCCRG*TVVFLKQLGRSLLLVTGPLILSRVPLLK<THQKFVITTSTKMDMSGVEIPEHLPEAYFRK
ParentalKK-LRKPRHQEGEIFDTEKEKYEITEQRKADQKAVDS-QILRRIKAVPQLQGYLRSV-FALTNGIYPHKL
K..L.KPR.QEGE.FDT...K.E.TEQ......AV.S.Q..R...AVPQLQG.L.S..F.LTN.IYPH.L
RetrocopyKQ>LGKPRYQEGEHFDTGTGKSEPTEQHRVNPRAVGS<QCCRKLTAVPQLQGDLCSE>FSLTNEIYPHRL
ParentalVF
VF
RetrocopyVF

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_100 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_100 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 21 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000030601 retrocopy
retro_acar_171,
Bos taurus ENSBTAG000000317236 retrocopies
retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris ENSCAFG000000088731 retrocopy
retro_cfam_36,
Callithrix jacchus ENSCJAG000000124507 retrocopies
retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus ENSCPOG000000135268 retrocopies
retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Equus caballus ENSECAG000000175141 retrocopy
retro_ecab_811,
Felis catus ENSFCAG0000000685812 retrocopies
retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Gorilla gorilla ENSGGOG0000000337216 retrocopies
retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Macaca mulatta ENSMMUG000000074331 retrocopy
retro_mmul_171,
Monodelphis domestica ENSMODG000000030964 retrocopies
retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furoENSMPUG000000025269 retrocopies
retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus ENSMUSG0000002961413 retrocopies
retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys ENSNLEG000000270932 retrocopies
retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus ENSOCUG000000038025 retrocopies
retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii ENSPPYG0000002585513 retrocopies
retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus ENSRNOG000000259361 retrocopy
retro_rnor_129,
Sarcophilus harrisii ENSSHAG000000070962 retrocopies
retro_shar_506, retro_shar_536,
Sus scrofa ENSSSCG000000248254 retrocopies
retro_sscr_1086, retro_sscr_1137, retro_sscr_397, retro_sscr_578,
Ictidomys tridecemlineatus ENSSTOG000000094093 retrocopies
retro_itri_1024, retro_itri_1125, retro_itri_684,
Tursiops truncatus ENSTTRG000000092687 retrocopies
retro_ttru_1053, retro_ttru_1428, retro_ttru_1827, retro_ttru_424, retro_ttru_608, retro_ttru_652, retro_ttru_954,
Vicugna pacos ENSVPAG00000007000 5 retrocopies
retro_vpac_100 , retro_vpac_184, retro_vpac_374, retro_vpac_623, retro_vpac_75,


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