RetrogeneDB ID:

retro_opri_561

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_17223:37460..37829(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL31
Ensembl ID:ENSOPRG00000001204
Aliases:None
Description:ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]


Retrocopy-Parental alignment summary:






>retro_opri_561
GCTCCCATAAAGAAGGGCAGAGAAAAGACAAAGGGCCATCAGCCTTCAACAAGGTGGTAACCCAGGAGTCCACCAACAAC
ATTCATAAGCGTGTCCACGGAGTGGGCCTCTAGAAGCGGTCCCCTCAAGCACTCAAAGAGATCTGCAAGTTTGCCATGAA
AGAGATGGGGGCTCCAGAAGTGCACATCAGTACCAGGCTCAACCAAGCTGCCCGGGCCAAAGGAATACAGAACGTTCCAT
ACCACACTGTGTGAGACTGTCCAGAAAACGTCATGAGGGTGAAGATCCACCTAACAAGCTCTCCACTTTGTTACCTGTGT
ACCTGTCACCACTTCCAAAAATCTGCAGTCCATGTGGATGACAACTAAC

ORF - retro_opri_561 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.72 %
Parental protein coverage: 99.2 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAPAKKGGEKKKGR-SAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
AP.KKG.EK.KG..SA.N.VVT.E.T.NIHKR.HGVG..KR.P.ALKEI.KFAMKEMG.P.V.I.TRLN.
RetrocopyAPIKKGREKTKGH<SAFNKVVTQESTNNIHKRVHGVGL*KRSPQALKEICKFAMKEMGAPEVHISTRLNQ
ParentalAVWAKGIRNVPYRI-RVRLSRKRNEDEDSPNKLYTL-VTYVPVTTFKNLQTVNVDEN
A..AKGI.NVPY....VRLSRKR.E.ED.PNKL.TL.VT.VPVTT.KNLQ......N
RetrocopyAARAKGIQNVPYHT<CVRLSRKRHEGEDPPNKLSTL<VTCVPVTTSKNLQSMWMTTN

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






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_561 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps 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 11 parental genes, and 239 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000156472 retrocopies
Latimeria chalumnae ENSLACG000000136031 retrocopy
Loxodonta africana ENSLAFG0000002787312 retrocopies
Macropus eugenii ENSMEUG000000009638 retrocopies
Myotis lucifugus ENSMLUG0000000250721 retrocopies
Otolemur garnettii ENSOGAG0000001449410 retrocopies
Ochotona princeps ENSOPRG00000001204 34 retrocopies
Pongo abelii ENSPPYG000000258704 retrocopies
Sus scrofa ENSSSCG000000081704 retrocopies
Sus scrofa ENSSSCG000000251806 retrocopies
Tupaia belangeri ENSTBEG00000016254137 retrocopies
retro_tbel_1092, retro_tbel_1129, retro_tbel_115, retro_tbel_1176, retro_tbel_1195, retro_tbel_1226, retro_tbel_1239, retro_tbel_1249, retro_tbel_1254, retro_tbel_1258, retro_tbel_1266, retro_tbel_131, retro_tbel_1310, retro_tbel_1334, retro_tbel_1356, retro_tbel_1368, retro_tbel_1369, retro_tbel_1381, retro_tbel_1402, retro_tbel_1414, retro_tbel_1423, retro_tbel_1437, retro_tbel_1454, retro_tbel_1574, retro_tbel_1593, retro_tbel_1597, retro_tbel_1605, retro_tbel_1611, retro_tbel_1612, retro_tbel_1632, retro_tbel_1768, retro_tbel_1797, retro_tbel_1802, retro_tbel_184, retro_tbel_189, retro_tbel_1890, retro_tbel_1897, retro_tbel_1915, retro_tbel_2024, retro_tbel_2027, retro_tbel_2050, retro_tbel_2069, retro_tbel_2093, retro_tbel_2140, retro_tbel_2159, retro_tbel_2233, retro_tbel_2341, retro_tbel_2359, retro_tbel_2382, retro_tbel_246, retro_tbel_2520, retro_tbel_2531, retro_tbel_2581, retro_tbel_2582, retro_tbel_2614, retro_tbel_2625, retro_tbel_2668, retro_tbel_2692, retro_tbel_2709, retro_tbel_2741, retro_tbel_2789, retro_tbel_2825, retro_tbel_2847, retro_tbel_2930, retro_tbel_2951, retro_tbel_3015, retro_tbel_3028, retro_tbel_3035, retro_tbel_3061, retro_tbel_3077, retro_tbel_3154, retro_tbel_3174, retro_tbel_3222, retro_tbel_3274, retro_tbel_3282, retro_tbel_3292, retro_tbel_3346, retro_tbel_3365, retro_tbel_337, retro_tbel_3378, retro_tbel_3425, retro_tbel_3442, retro_tbel_3484, retro_tbel_3500, retro_tbel_3519, retro_tbel_3578, retro_tbel_3580, retro_tbel_3618, retro_tbel_3637, retro_tbel_3710, retro_tbel_3722, retro_tbel_3745, retro_tbel_3775, retro_tbel_3780, retro_tbel_3794, retro_tbel_3801, retro_tbel_381, retro_tbel_3812, retro_tbel_3846, retro_tbel_3869, retro_tbel_3873, retro_tbel_398, retro_tbel_3982, retro_tbel_3996, retro_tbel_4033, retro_tbel_4069, retro_tbel_4158, retro_tbel_4161, retro_tbel_4174, retro_tbel_4235, retro_tbel_4247, retro_tbel_4286, retro_tbel_4297, retro_tbel_4363, retro_tbel_4374, retro_tbel_461, retro_tbel_4612, retro_tbel_4646, retro_tbel_466, retro_tbel_488, retro_tbel_503, retro_tbel_510, retro_tbel_577, retro_tbel_599, retro_tbel_626, retro_tbel_696, retro_tbel_718, retro_tbel_741, retro_tbel_744, retro_tbel_780, retro_tbel_788, retro_tbel_872, retro_tbel_886, retro_tbel_891, retro_tbel_908, retro_tbel_914, retro_tbel_942,



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