RetrogeneDB ID:

retro_vpac_129

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_1993:1801665..1802123(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL21
Ensembl ID:ENSVPAG00000006206
Aliases:None
Description:ribosomal protein L21 [Source:HGNC Symbol;Acc:10313]


Retrocopy-Parental alignment summary:






>retro_vpac_129
ATGAATAACCCAAAGAGAAAGAGGAGAGGCACCTGCTATGTGTTTTCTAGGCCTTTTAGAAAACATGGAGGTGTTCTTTT
GGCAACATACACGCAAACCTACAAGAAAGGTGATTCTGTAGACCTCAAGGCTGGGCACTGCTCAAAAGGAATAACCAACA
AATGTTACCAGGGCAAAACCGGAAGAGTCCAGAGTATACTTAGCAGACTTGCTGGCAAACTGAAACACGTTAAGGGCAAG
ATTCTTGCCAAGAGGATTGATGCTCGTACAATCTATAGCAGCAGAAATAGCTTCCTGAAACTTGTGAAGGAAAATGATCA
GTAAAGAAGGAAGCCGAAGAGAAAGGGACCTGGGTTCACTTGAAGCCCCAGCCTGCTCCCCGAAGAGAAGCACACTTCGT
GAGAACTAGCGGGAAGGAGCCTGAGCTGCTGGAATCTGTTCCTTATGAATTCCTGGCA

ORF - retro_vpac_129 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.6 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGTGTVQKGMPHKCYHGKTGRVYNVTQH
M.N.K.KRRGT.Y.FSRPFRKHG.V.LATY...YKKGD.VD.K..G...KG...KCY.GKTGRV......
RetrocopyMNNPKRKRRGTCYVFSRPFRKHGGVLLATYTQTYKKGDSVDLKA-GHCSKGITNKCYQGKTGRVQSILSR
ParentalAVGIIVNKQVKGKILAKRINVRVEHIKHSKSRDSFLKRVRENDQ-KKKEAKEKGTWVQLKRQPAPPREAH
..G....K.VKGKILAKRI..R........SR.SFLK.V.ENDQ..KKEA.EKGTWV.LK.QPAP.REAH
RetrocopyLAGKL--KHVKGKILAKRIDARTIY----SSRNSFLKLVKENDQ<VKKEAEEKGTWVHLKPQPAPRREAH
ParentalFVRTNGKEPELLEPIPYEFMA
FVRT.GKEPELLE..PYEF.A
RetrocopyFVRTSGKEPELLESVPYEFLA

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_129 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_129 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 24 parental genes, and 276 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000016485 retrocopies
Choloepus hoffmanni ENSCHOG000000078676 retrocopies
Callithrix jacchus ENSCJAG000000193551 retrocopy
Cavia porcellus ENSCPOG000000087843 retrocopies
Equus caballus ENSECAG000000106615 retrocopies
Felis catus ENSFCAG000000067501 retrocopy
Latimeria chalumnae ENSLACG000000126781 retrocopy
Loxodonta africana ENSLAFG0000000367711 retrocopies
Myotis lucifugus ENSMLUG0000001009346 retrocopies
Macaca mulatta ENSMMUG000000233682 retrocopies
Macaca mulatta ENSMMUG000000295742 retrocopies
Monodelphis domestica ENSMODG000000089231 retrocopy
Mustela putorius furoENSMPUG0000000935323 retrocopies
Mus musculus ENSMUSG00000041453101 retrocopies
retro_mmus_1012, retro_mmus_1046, retro_mmus_1057, retro_mmus_1083, retro_mmus_1123, retro_mmus_1199, retro_mmus_1287, retro_mmus_1354, retro_mmus_1461, retro_mmus_1475, retro_mmus_1529, retro_mmus_1561, retro_mmus_1572, retro_mmus_1596, retro_mmus_1617, retro_mmus_1641, retro_mmus_1644, retro_mmus_17, retro_mmus_1714, retro_mmus_1739, retro_mmus_1762, retro_mmus_1797, retro_mmus_1848, retro_mmus_1860, retro_mmus_1862, retro_mmus_1875, retro_mmus_1897, retro_mmus_1915, retro_mmus_1931, retro_mmus_1936, retro_mmus_1994, retro_mmus_2042, retro_mmus_2049, retro_mmus_2101, retro_mmus_2130, retro_mmus_2176, retro_mmus_2179, retro_mmus_2185, retro_mmus_2214, retro_mmus_2233, retro_mmus_2237, retro_mmus_2238, retro_mmus_2279, retro_mmus_2309, retro_mmus_2312, retro_mmus_2335, retro_mmus_2344, retro_mmus_2395, retro_mmus_2447, retro_mmus_2517, retro_mmus_2567, retro_mmus_2585, retro_mmus_2598, retro_mmus_266, retro_mmus_2662, retro_mmus_2698, retro_mmus_2707, retro_mmus_2778, retro_mmus_2808, retro_mmus_2853, retro_mmus_2874, retro_mmus_2945, retro_mmus_2980, retro_mmus_3035, retro_mmus_3055, retro_mmus_3085, retro_mmus_3103, retro_mmus_3112, retro_mmus_3220, retro_mmus_3252, retro_mmus_3261, retro_mmus_3295, retro_mmus_3318, retro_mmus_3328, retro_mmus_333, retro_mmus_3341, retro_mmus_3446, retro_mmus_3545, retro_mmus_3581, retro_mmus_3712, retro_mmus_397, retro_mmus_400, retro_mmus_401, retro_mmus_598, retro_mmus_601, retro_mmus_606, retro_mmus_663, retro_mmus_734, retro_mmus_735, retro_mmus_758, retro_mmus_782, retro_mmus_806, retro_mmus_835, retro_mmus_862, retro_mmus_883, retro_mmus_918, retro_mmus_932, retro_mmus_940, retro_mmus_957, retro_mmus_993, retro_mmus_998,
Nomascus leucogenys ENSNLEG000000003276 retrocopies
Oryctolagus cuniculus ENSOCUG0000000250610 retrocopies
Otolemur garnettii ENSOGAG000000339364 retrocopies
Otolemur garnettii ENSOGAG000000344231 retrocopy
Pongo abelii ENSPPYG000000052337 retrocopies
Pongo abelii ENSPPYG000000061672 retrocopies
Pan troglodytes ENSPTRG000000057281 retrocopy
Rattus norvegicus ENSRNOG0000000095713 retrocopies
Sarcophilus harrisii ENSSHAG0000000084511 retrocopies
Vicugna pacos ENSVPAG00000006206 13 retrocopies



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