RetrogeneDB ID:

retro_pvam_589

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_3936:536754..537231(-)
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:ENSPVAG00000000077
Aliases:None
Description:ribosomal protein L21 [Source:HGNC Symbol;Acc:10313]


Retrocopy-Parental alignment summary:






>retro_pvam_589
ATGACCAACACACAGGGAAAGAGGAGAGGCACCCGCTATTTGTTCTCTAGGCCTTTTAGAAAATATGAGTTGTCCCTTTG
GCCAAATACATGCAAATCTATAAGAAAGGTGACATTGTAGACATCGAGGGAGTGGGCACTGCTCTAAAGGAACGCCCCAC
AAATACTACCATGGCAAAACTGGAAGAGTTTACAGTGTCACCCAGCATGCAGTTGGCATTGTTGTAAACAAACAAGTTAA
GGGCAAGATTGTTGCCAAGAGAATTAATGTATGTATTGAGCATATTAAGCAATCTAAGTGCCGAGATCGCTTCCTGAAAC
TTGAAGGAAAATGACTGAAAAAAGGAAGCCGAAGAGAAAGGTACCTGGGTTCAGCTGAAGCACCAGCCTACTCCACCCAG
AGCAAGCAGCTCACTGTGTGAGAACAAATGGGAAGGAGCCTGAGCTGCTGGAGCCCATTCCCTATGAATTCATGGCA

ORF - retro_pvam_589 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.27 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFSRPFRKHG-VVPLATYMRIYKKGDIVDIKGMGTV-QKGMPHKCYHGKTGRVYNVT
MTNT.GKRRGTRY.FSRPFRK...VVPLA.YM.IYKKGDIVDI.G.GT...KG.PHK.YHGKTGRVY.VT
RetrocopyMTNTQGKRRGTRYLFSRPFRKYE<VVPLAKYMQIYKKGDIVDIEGVGTA<SKGTPHKYYHGKTGRVYSVT
ParentalQHAVGIVVNK-QVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAP-PR
QHAVGIVVNK.......L..........I....S........KEND.KK.EA.EKGTWVQLK.QP.P.P.
RetrocopyQHAVGIVVNK>KLRARLLPREL-MYVLSILSNLSAEIAS*NLKEND*KK-EAEEKGTWVQLKHQPTP>PE
ParentalEA-HFVRTNGKEPELLEPIPYEFMA
.A.H.VRTNGKEPELLEPIPYEFMA
RetrocopyQAAHCVRTNGKEPELLEPIPYEFMA

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






Pteropus vampyrus was not studied using RNA-Seq expression data.
Pteropus vampyrus was not studied using ChIP-Seq data.
Pteropus vampyrus was not studied using EST data.
Pteropus vampyrus was not studied using FANTOM5 data.
retro_pvam_589 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus 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 17 parental genes, and 300 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000016485 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
Monodelphis domestica ENSMODG000000089231 retrocopy
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
Pan troglodytes ENSPTRG000000057281 retrocopy
Pteropus vampyrus ENSPVAG00000000077 82 retrocopies
Rattus norvegicus ENSRNOG0000000095713 retrocopies
Sarcophilus harrisii ENSSHAG0000000084511 retrocopies



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