RetrogeneDB ID:

retro_vpac_174

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_2392:302711..303184(-)
Located in intron of:ENSVPAG00000001994
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_174
ATGACCAACACAAAAGGAAAGAGGAGACTTCGCTATATGTTCTCTTATGCCTTTTAGAAAACAGGGTGTTGTTCCTTTGG
CCACATATATGGAAATCTACAAGAAAGGTAGATATTGTAGGTATCAAGGGAATGGGTACTGTTCAAAAAGGAATGCCCCA
CAAATGTTACCAGGGCAAAACTGGAAGTCTACAATGTTACCCAGCATGCTGTTGGCATTGTTGTAAGCAAACAAGTTAAG
GGCAAGAGTCTTGCCAAGAGAATTAATGTGTATACTGAGCATATTAAACACTCCAAGAGCTAAGATAGCTTCCCAAAACA
AGCGAAGGAAAATGATCAAAGAAGAAAGCCAAAGAGAAAGGTACTTGGGTTCAAATGAAGTGCCAGCCTGCTCCACCCAG
AGAAGCACACTTTGTGAGAACCAATGGAAAGAAGCCTGAATTGTTGGAACTCATTCCCTATAAATTCATGGCA

ORF - retro_vpac_174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.39 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFS-RPFRKHGVVPLATYMRIYKKG-DIVDIKGTGTVQ-KGMPHKCYHGKTGRVYNV
MTNTKGKRR..RYMFS..PFRK.GVVPLATYM.IYKKG.DIV.IKG.GTVQ.K..P......K...VYNV
RetrocopyMTNTKGKRR-LRYMFS>MPFRKQGVVPLATYMEIYKKG>DIVGIKGMGTVQ>KECPTNVTRAKL-EVYNV
ParentalTQHAVGIIVNKQVKGKILAKRINVRVEHIKHSKSRDSFLKRVRENDQKKKEAKEK-GTWVQLKRQPAPPR
TQHAVGI.V.KQVKGK.LAKRINV..EHIKHSKS.DSF.K...ENDQ..K..K.K.GTWVQ.K.QPAPPR
RetrocopyTQHAVGIVVSKQVKGKSLAKRINVYTEHIKHSKS*DSFPKQAKENDQRRK-PKRK<GTWVQMKCQPAPPR
ParentalEAHFVRTNGKEPELLEPIPYEFMA
EAHFVRTNGK.PELLE.IPY.FMA
RetrocopyEAHFVRTNGKKPELLELIPYKFMA

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_174 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_174 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
retro_btau_1383, retro_btau_194, retro_btau_209, retro_btau_93, retro_btau_976,
Choloepus hoffmanni ENSCHOG000000078676 retrocopies
retro_chof_1472, retro_chof_1596, retro_chof_2421, retro_chof_2454, retro_chof_266, retro_chof_572,
Callithrix jacchus ENSCJAG000000193551 retrocopy
retro_cjac_152,
Cavia porcellus ENSCPOG000000087843 retrocopies
retro_cpor_2, retro_cpor_26, retro_cpor_41,
Equus caballus ENSECAG000000106615 retrocopies
retro_ecab_16, retro_ecab_24, retro_ecab_39, retro_ecab_88, retro_ecab_90,
Felis catus ENSFCAG000000067501 retrocopy
retro_fcat_64,
Latimeria chalumnae ENSLACG000000126781 retrocopy
retro_lcha_32,
Loxodonta africana ENSLAFG0000000367711 retrocopies
retro_lafr_1167, retro_lafr_308, retro_lafr_331, retro_lafr_583, retro_lafr_63, retro_lafr_652, retro_lafr_738, retro_lafr_740, retro_lafr_856, retro_lafr_89, retro_lafr_97,
Myotis lucifugus ENSMLUG0000001009346 retrocopies
retro_mluc_1066, retro_mluc_1079, retro_mluc_1138, retro_mluc_1164, retro_mluc_1171, retro_mluc_1219, retro_mluc_1274, retro_mluc_1279, retro_mluc_1307, retro_mluc_1323, retro_mluc_1379, retro_mluc_1382, retro_mluc_1409, retro_mluc_1413, retro_mluc_1469, retro_mluc_1481, retro_mluc_1525, retro_mluc_162, retro_mluc_1647, retro_mluc_1753, retro_mluc_1803, retro_mluc_1849, retro_mluc_1862, retro_mluc_1929, retro_mluc_1969, retro_mluc_1981, retro_mluc_2044, retro_mluc_2077, retro_mluc_2109, retro_mluc_2121, retro_mluc_2212, retro_mluc_230, retro_mluc_2335, retro_mluc_2338, retro_mluc_2436, retro_mluc_2592, retro_mluc_27, retro_mluc_279, retro_mluc_360, retro_mluc_503, retro_mluc_554, retro_mluc_620, retro_mluc_631, retro_mluc_806, retro_mluc_961, retro_mluc_97,
Macaca mulatta ENSMMUG000000233682 retrocopies
retro_mmul_288, retro_mmul_45,
Macaca mulatta ENSMMUG000000295742 retrocopies
retro_mmul_1289, retro_mmul_219,
Monodelphis domestica ENSMODG000000089231 retrocopy
retro_mdom_156,
Mustela putorius furoENSMPUG0000000935323 retrocopies
retro_mputfur_1083, retro_mputfur_1117, retro_mputfur_1203, retro_mputfur_1342, retro_mputfur_1345, retro_mputfur_1498, retro_mputfur_196, retro_mputfur_208, retro_mputfur_248, retro_mputfur_256, retro_mputfur_310, retro_mputfur_311, retro_mputfur_398, retro_mputfur_580, retro_mputfur_584, retro_mputfur_699, retro_mputfur_700, retro_mputfur_796, retro_mputfur_806, retro_mputfur_903, retro_mputfur_934, retro_mputfur_991, retro_mputfur_992,
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
retro_nleu_112, retro_nleu_1144, retro_nleu_26, retro_nleu_713, retro_nleu_95, retro_nleu_951,
Oryctolagus cuniculus ENSOCUG0000000250610 retrocopies
retro_ocun_104, retro_ocun_122, retro_ocun_125, retro_ocun_159, retro_ocun_163, retro_ocun_186, retro_ocun_198, retro_ocun_209, retro_ocun_232, retro_ocun_86,
Otolemur garnettii ENSOGAG000000339364 retrocopies
retro_ogar_1787, retro_ogar_2621, retro_ogar_3093, retro_ogar_416,
Otolemur garnettii ENSOGAG000000344231 retrocopy
retro_ogar_3296,
Pongo abelii ENSPPYG000000052337 retrocopies
retro_pabe_1173, retro_pabe_1404, retro_pabe_1437, retro_pabe_3494, retro_pabe_52, retro_pabe_54, retro_pabe_65,
Pongo abelii ENSPPYG000000061672 retrocopies
retro_pabe_1617, retro_pabe_327,
Pan troglodytes ENSPTRG000000057281 retrocopy
retro_ptro_66,
Rattus norvegicus ENSRNOG0000000095713 retrocopies
retro_rnor_227, retro_rnor_298, retro_rnor_319, retro_rnor_329, retro_rnor_330, retro_rnor_333, retro_rnor_365, retro_rnor_366, retro_rnor_416, retro_rnor_5, retro_rnor_79, retro_rnor_81, retro_rnor_82,
Sarcophilus harrisii ENSSHAG0000000084511 retrocopies
retro_shar_224, retro_shar_446, retro_shar_499, retro_shar_531, retro_shar_534, retro_shar_601, retro_shar_664, retro_shar_67, retro_shar_683, retro_shar_729, retro_shar_757,
Vicugna pacos ENSVPAG00000006206 13 retrocopies
retro_vpac_129, retro_vpac_140, retro_vpac_147, retro_vpac_174 , retro_vpac_187, retro_vpac_273, retro_vpac_298, retro_vpac_388, retro_vpac_394, retro_vpac_593, retro_vpac_600, retro_vpac_61, retro_vpac_633,


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