RetrogeneDB ID:

retro_opri_835

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_3555:140429..140810(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL12
Ensembl ID:ENSOPRG00000011078
Aliases:None
Description:ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]


Retrocopy-Parental alignment summary:






>retro_opri_835
GGTGAGGTGGGTACCACGTCCGCCCTAGCCCCCAAAATTGGCCCCCTGGGTCTGTCTCTGAAGAAGGTGGAAGATGACAT
TGCAGAGCCTGTGGGGACTGGAAGGGCCTGCGGATCAGGTAAAACTGACCATCCAGAGCCAACAAGTGCATATTGAGGTG
GTGCCATCAGCCTCTGTCCTGATTATCAAGGCCCTCAAGGAGCCACTGAGGGACTGCAAGAAGCAGAAGAACATCAAACA
CAGTGGGAAAATCACATTTGATGAAATTGTCAACATCGTCTGTAGGTGCGCCACAAATTCTTAGCCAGAGAACTTTCTGG
AACCATCAAAGAGATTCTGGAGACTGCCCAGTCAATGAATTGTAACGTGGATGGCTGCCAC

ORF - retro_opri_835 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.63 %
Parental protein coverage: 77.44 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGEVGATSALAPKIGPLGLSPKKVGDDIA-KATGDWKGLRIT-VKLTIQNRQAQIEVVPSASALII-ALKE
GEVG.TSALAPKIGPLGLS.KKV.DDIA..A.GDWKGLRI..VKLTIQ..Q..IEVVPSAS.LII.ALKE
RetrocopyGEVGTTSALAPKIGPLGLSLKKVEDDIA<RACGDWKGLRIR<VKLTIQSQQVHIEVVPSASVLIIKALKE
ParentalPPRDRKKQKNIKHSGNITFDEIVNIARQ-MRHRSLARELSGTIKEILGTAQSVGCNVDGRH
P.RD.KKQKNIKHSG.ITFDEIVNI.....RH..LARELSGTIKEIL.TAQS..CNVDG.H
RetrocopyPLRDCKKQKNIKHSGKITFDEIVNIVCR<VRHKFLARELSGTIKEILETAQSMNCNVDGCH

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_835 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 15 parental genes, and 279 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000069633 retrocopies
Callithrix jacchus ENSCJAG000000180821 retrocopy
Homo sapiens ENSG0000019795841 retrocopies
Latimeria chalumnae ENSLACG000000153733 retrocopies
Macropus eugenii ENSMEUG0000000738012 retrocopies
Macaca mulatta ENSMMUG000000004222 retrocopies
Monodelphis domestica ENSMODG000000045719 retrocopies
Mus musculus ENSMUSG000000389001 retrocopy
Oryctolagus cuniculus ENSOCUG000000049029 retrocopies
Otolemur garnettii ENSOGAG00000000597120 retrocopies
retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Ochotona princeps ENSOPRG00000011078 21 retrocopies
Pongo abelii ENSPPYG0000001962244 retrocopies
Pan troglodytes ENSPTRG000000228081 retrocopy
Rattus norvegicus ENSRNOG000000162204 retrocopies
Sarcophilus harrisii ENSSHAG000000178648 retrocopies



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