RetrogeneDB ID:

retro_vpac_175

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_2417:78898..79892(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHA
Ensembl ID:ENSVPAG00000010215
Aliases:None
Description:lactate dehydrogenase A [Source:HGNC Symbol;Acc:6535]


Retrocopy-Parental alignment summary:






>retro_vpac_175
ATGGCAACTCTTAAGGAAAAGCTGATCGCACCAGTTGCAGAAGGAGAGGCAATGGTCCCCAACAGTAAGATCACTGTAGT
GGGTGCTGGAAAGTTGGCACAGCATGTGCCATCAGCATTTTGGGAAAGTCTCTGGCTGATGAGCTTGCTCTTGTGGATAT
TTTGGAAGATAAACACAAAGGCAAAATGACGGATCTTCTGCATGGGGCTTGTTTCTTCAGACACCAAAAAAATGTGGCAG
ATAAAGATTACTCTGTGACCGCCAATCTCAAGTTTGTGGTTTTGACTGCAGGAGTTCTCCAGCAAGAGGGGGAGAGTTGT
CTCAATCTGGTGCAGAGGAACGTTAATGTCTTCAAGTTCATCATTCCTCAGATCATCAAGTACAGTCCTGATTGCATCAT
AATTGTGGTTTCTAACCCAGTGGATATTCTCACATATATTACCTGGAGACTAACTGTATTACCCAAACACTGTGTGATTG
AAAATGGGTGTAGTCTGGATTCTACTAGATTCCGTTATCTTATGGCGGAAAAAGTTGGCATTCATCCCAGCAGCTGCCAT
GGATGGATTTTGGGAGAACATGGCAACTCAAGTGTGGTTATGTGGAGTGGGGTGAAAGTGGCAGCCGTTTCTCTCCAGGA
ACTGAATCCAGAAATGGGAATGGACAATGATAGTGAAAATTGGAAGGAGTGCATAAGATGGTGGTTAACAGTGCCTATGA
AGTCATCAACCTAAAGGGGTACACCAACTGGGCTATTAGATTAAGTGTGGCTGATAGTATTGAATCCGTGTTGAAAAATA
TCTCCAGGATTCACCCAGTGCCAGCAATGGTAAGGGGGATGTATGACATCGAGAATGAAGTCTTCCTGAGCTTTCCATGT
ATCCTGAATGCTTGAGGATTAACCAGTTTTATCAACCAGAAGCTGAAGGATGATGAGGTTGCCCAACACAAGAAAAGTGC
AGACACCCTATGGGACATCCAGAAGGATCTAAAG

ORF - retro_vpac_175 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.38 %
Parental protein coverage: 99.7 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMATLKDQLIQNLLK-EEHVPQNKITVVGVGA-VGMACAISILMK-LADELALVDVMEDKLKGEMMDLQHG
MATLK..LI......E..VP..KITVVG.G..VG.ACAISIL.K.LADELALVD..EDK.KG.M.DL.HG
RetrocopyMATLKEKLIAPVAEGEAMVPNSKITVVGAGK<VGTACAISILGKSLADELALVDILEDKHKGKMTDLLHG
ParentalSLFLRTPKIVSGKDYNVTANSRLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLVVSN
..F.R..K.V..KDY.VTAN...V..TAG..QQEGES.LNLVQRNVN.FKFIIP...KYSP.C...VVSN
RetrocopyACFFRHQKNVADKDYSVTANLKFVVLTAGVLQQEGESCLNLVQRNVNVFKFIIPQIIKYSPDCIIIVVSN
ParentalP-DILTYVA-KISGFPKNRVIGSGCNLDSARFRYVMGERLGVHPLSCHGWILGEHGDSSVPVWSGINVAG
P.DILTY........PK..VI..GC.LDS.RFRY.M.E..G.HP.SCHGWILGEHG.SSV..WSG..VA.
RetrocopyPVDILTYITWRLTVLPKHCVIENGCSLDSTRFRYLMAEKVGIHPSSCHGWILGEHGNSSVVMWSGVKVAA
ParentalVSLKNLHPELGTDADKEQWK-AVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMI
VSL..L.PE.G.D.D.E.WK..VHK.VV.SAYEVI.LKGYT.WAI.LSVAD..ES..KN..R.HP...M.
RetrocopyVSLQELNPEMGMDNDSENWK<GVHKMVVNSAYEVINLKGYTNWAIRLSVADSIESVLKNISRIHPVPAMV
ParentalKGLYGIKEDVFLSVPCILGQNGISDVVKVTLTPEEEAHLKKSADTLWGIQKELQ
.G.Y.I...VFLS.PCIL...G........L...E.A..KKSADTLW.IQK.L.
RetrocopyRGMYDIENEVFLSFPCILNA*GLTSFINQKLKDDEVAQHKKSADTLWDIQKDLK

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_175 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_175 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 26 parental genes, and 221 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178542 retrocopies
Bos taurus ENSBTAG000000086832 retrocopies
Choloepus hoffmanni ENSCHOG0000000997714 retrocopies
Callithrix jacchus ENSCJAG000000070941 retrocopy
Cavia porcellus ENSCPOG000000119262 retrocopies
Dasypus novemcinctus ENSDNOG0000001891511 retrocopies
Equus caballus ENSECAG000000206695 retrocopies
Echinops telfairi ENSETEG0000000750815 retrocopies
Homo sapiens ENSG000001343335 retrocopies
Gorilla gorilla ENSGGOG000000103503 retrocopies
Loxodonta africana ENSLAFG000000113071 retrocopy
Macropus eugenii ENSMEUG0000000146291 retrocopies
retro_meug_101, retro_meug_1029, retro_meug_103, retro_meug_1082, retro_meug_1088, retro_meug_1105, retro_meug_1140, retro_meug_1162, retro_meug_1189, retro_meug_1190, retro_meug_1260, retro_meug_1288, retro_meug_1295, retro_meug_1301, retro_meug_1323, retro_meug_1329, retro_meug_1332, retro_meug_1356, retro_meug_1368, retro_meug_1376, retro_meug_1400, retro_meug_1402, retro_meug_1404, retro_meug_1417, retro_meug_1419, retro_meug_1420, retro_meug_1422, retro_meug_1484, retro_meug_1535, retro_meug_155, retro_meug_1556, retro_meug_1620, retro_meug_1632, retro_meug_1652, retro_meug_1674, retro_meug_1685, retro_meug_1720, retro_meug_1721, retro_meug_1747, retro_meug_1749, retro_meug_1765, retro_meug_1779, retro_meug_1781, retro_meug_181, retro_meug_1824, retro_meug_1875, retro_meug_1898, retro_meug_1906, retro_meug_1915, retro_meug_1927, retro_meug_1945, retro_meug_1977, retro_meug_200, retro_meug_2000, retro_meug_2022, retro_meug_2067, retro_meug_2107, retro_meug_2126, retro_meug_2137, retro_meug_2139, retro_meug_2168, retro_meug_226, retro_meug_244, retro_meug_291, retro_meug_336, retro_meug_351, retro_meug_436, retro_meug_448, retro_meug_477, retro_meug_532, retro_meug_572, retro_meug_590, retro_meug_591, retro_meug_626, retro_meug_634, retro_meug_638, retro_meug_639, retro_meug_660, retro_meug_68, retro_meug_736, retro_meug_737, retro_meug_832, retro_meug_861, retro_meug_867, retro_meug_870, retro_meug_891, retro_meug_916, retro_meug_927, retro_meug_971, retro_meug_980, retro_meug_981,
Macaca mulatta ENSMMUG000000310242 retrocopies
Monodelphis domestica ENSMODG000000065222 retrocopies
Mus musculus ENSMUSG0000006322914 retrocopies
Nomascus leucogenys ENSNLEG000000177674 retrocopies
Oryctolagus cuniculus ENSOCUG000000159396 retrocopies
Pongo abelii ENSPPYG000000034375 retrocopies
Pan troglodytes ENSPTRG000000034215 retrocopies
Rattus norvegicus ENSRNOG0000001300917 retrocopies
Sorex araneus ENSSARG000000012241 retrocopy
Sarcophilus harrisii ENSSHAG000000157761 retrocopy
Sus scrofa ENSSSCG000000133661 retrocopy
Tarsius syrichta ENSTSYG000000080624 retrocopies
Tursiops truncatus ENSTTRG000000137562 retrocopies
Vicugna pacos ENSVPAG00000010215 5 retrocopies



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