RetrogeneDB ID:

retro_opri_1226

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_9966:47339..47739(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RSL24D1
Ensembl ID:ENSOPRG00000013115
Aliases:None
Description:ribosomal L24 domain containing 1 [Source:HGNC Symbol;Acc:18479]


Retrocopy-Parental alignment summary:






>retro_opri_1226
GTGTTTAGATTCTGTAAATCCAAATGTCATAAAAACTTTAAAAAGAAGCGTAATCCTCGCAAGGTCAGGTGGGCCAAAGC
ATTCCGGAAAGCAGCCGGCAAGGAACTGACAGTGGATAATTCATTTGATTTGAAAAACGAAGAAATGAACCTATCAAATA
CCAGAGAGAGTGTGGATAAAACTATTGATGCAATGAAGAGAGTTGAAGAGATGTAGCAGAAAAGCCAAGCTAAATTTATA
ATGAACAGATTGAAGAAAAATAAAGAACTACAGAAAGATTAGGACATCAAAGAAGTCAAGCAGAATATTCACCTCATCCG
GGCTCCTGTTGCAGGCAAACAGCTGGAAAGAAAAAAATGGTACAGCAGGTACAAGAAAGATGTGGACATGGGAGGATACT

ORF - retro_opri_1226 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.73 %
Parental protein coverage: 99.26 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalVFRFCKSKCHKNFKKKRNPRKVRWTKAFRKAAGKELTVDNSFE-FEKRRNEPVKYQRE-LW-NKTIDAMK
VFRFCKSKCHKNFKKKRNPRKVRW.KAFRKAAGKELTVDNSF..FEKRRNEP.KYQRE..W..KTIDAMK
RetrocopyVFRFCKSKCHKNFKKKRNPRKVRWAKAFRKAAGKELTVDNSFD<FEKRRNEPIKYQRE<VW<DKTIDAMK
ParentalRVEEIKQKRQAKFIMNRLKKNKELQKVQDIKEVKQNIHLIRAPVAKGKQLE-DKMVQQLQEDVDM-EDT
RVEE..QK.QAKFIMNRLKKNKELQK..DIKEVKQNIHLIRAPVA.GKQLE..K.......DVDM.EDT
RetrocopyRVEEM*QKSQAKFIMNRLKKNKELQKD*DIKEVKQNIHLIRAPVA-GKQLERKKWYSRYKKDVDM>EDT

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






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

retro_opri_1226 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 29 parental genes, and 171 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000013421 retrocopy
retro_btau_1304,
Canis familiaris ENSCAFG000000159041 retrocopy
retro_cfam_1744,
Choloepus hoffmanni ENSCHOG000000117999 retrocopies
retro_chof_112, retro_chof_1237, retro_chof_1314, retro_chof_1357, retro_chof_1938, retro_chof_243, retro_chof_67, retro_chof_809, retro_chof_896,
Callithrix jacchus ENSCJAG000000007952 retrocopies
retro_cjac_109, retro_cjac_7,
Dasypus novemcinctus ENSDNOG000000108122 retrocopies
retro_dnov_858, retro_dnov_954,
Equus caballus ENSECAG000000188611 retrocopy
retro_ecab_30,
Erinaceus europaeus ENSEEUG000000067551 retrocopy
retro_eeur_50,
Felis catus ENSFCAG000000192721 retrocopy
retro_fcat_851,
Homo sapiens ENSG0000013787617 retrocopies
retro_hsap_1049, retro_hsap_1125, retro_hsap_1355, retro_hsap_1635, retro_hsap_1829, retro_hsap_1887, retro_hsap_1941, retro_hsap_1963, retro_hsap_2268, retro_hsap_2467, retro_hsap_3378, retro_hsap_338, retro_hsap_3566, retro_hsap_3861, retro_hsap_4015, retro_hsap_4101, retro_hsap_894,
Gorilla gorilla ENSGGOG0000000519515 retrocopies
retro_ggor_1055, retro_ggor_1081, retro_ggor_1151, retro_ggor_1194, retro_ggor_1235, retro_ggor_1412, retro_ggor_1536, retro_ggor_1688, retro_ggor_2286, retro_ggor_2406, retro_ggor_2600, retro_ggor_2697, retro_ggor_2754, retro_ggor_359, retro_ggor_879,
Microcebus murinus ENSMICG000000026213 retrocopies
retro_mmur_1378, retro_mmur_306, retro_mmur_952,
Myotis lucifugus ENSMLUG000000119764 retrocopies
retro_mluc_1415, retro_mluc_1512, retro_mluc_2173, retro_mluc_2320,
Macaca mulatta ENSMMUG0000002069316 retrocopies
retro_mmul_1030, retro_mmul_1107, retro_mmul_1257, retro_mmul_1363, retro_mmul_1406, retro_mmul_1560, retro_mmul_1824, retro_mmul_1907, retro_mmul_2105, retro_mmul_2364, retro_mmul_322, retro_mmul_424, retro_mmul_582, retro_mmul_599, retro_mmul_817, retro_mmul_872,
Monodelphis domestica ENSMODG000000079661 retrocopy
retro_mdom_825,
Mustela putorius furoENSMPUG000000022281 retrocopy
retro_mputfur_514,
Mus musculus ENSMUSG000000322151 retrocopy
retro_mmus_1695,
Nomascus leucogenys ENSNLEG0000000657816 retrocopies
retro_nleu_1289, retro_nleu_1321, retro_nleu_1392, retro_nleu_1468, retro_nleu_1779, retro_nleu_1809, retro_nleu_185, retro_nleu_2309, retro_nleu_2449, retro_nleu_2606, retro_nleu_2874, retro_nleu_2974, retro_nleu_386, retro_nleu_570, retro_nleu_919, retro_nleu_967,
Oryctolagus cuniculus ENSOCUG000000074472 retrocopies
retro_ocun_1108, retro_ocun_1899,
Otolemur garnettii ENSOGAG0000001040015 retrocopies
retro_ogar_1135, retro_ogar_1320, retro_ogar_1433, retro_ogar_1539, retro_ogar_1876, retro_ogar_1947, retro_ogar_2088, retro_ogar_2171, retro_ogar_2579, retro_ogar_3029, retro_ogar_3154, retro_ogar_3174, retro_ogar_3239, retro_ogar_3445, retro_ogar_619,
Ochotona princeps ENSOPRG00000013115 4 retrocopies
retro_opri_1047, retro_opri_1226 , retro_opri_66, retro_opri_777,
Pongo abelii ENSPPYG0000000649519 retrocopies
retro_pabe_1123, retro_pabe_1350, retro_pabe_1499, retro_pabe_1568, retro_pabe_1602, retro_pabe_1614, retro_pabe_1623, retro_pabe_1726, retro_pabe_1819, retro_pabe_1873, retro_pabe_1949, retro_pabe_2774, retro_pabe_2939, retro_pabe_3046, retro_pabe_3297, retro_pabe_3359, retro_pabe_771, retro_pabe_875, retro_pabe_930,
Pan troglodytes ENSPTRG0000000709416 retrocopies
retro_ptro_1103, retro_ptro_1164, retro_ptro_1268, retro_ptro_1296, retro_ptro_1311, retro_ptro_1426, retro_ptro_1607, retro_ptro_2422, retro_ptro_2631, retro_ptro_270, retro_ptro_2725, retro_ptro_2783, retro_ptro_617, retro_ptro_679, retro_ptro_715, retro_ptro_929,
Pteropus vampyrus ENSPVAG000000040933 retrocopies
retro_pvam_331, retro_pvam_619, retro_pvam_671,
Rattus norvegicus ENSRNOG000000076302 retrocopies
retro_rnor_1945, retro_rnor_506,
Sarcophilus harrisii ENSSHAG000000114941 retrocopy
retro_shar_465,
Sus scrofa ENSSSCG000000249831 retrocopy
retro_sscr_916,
Ictidomys tridecemlineatus ENSSTOG000000094086 retrocopies
retro_itri_100, retro_itri_1246, retro_itri_1388, retro_itri_1605, retro_itri_1699, retro_itri_1767,
Tupaia belangeri ENSTBEG000000107509 retrocopies
retro_tbel_1552, retro_tbel_2292, retro_tbel_3033, retro_tbel_4025, retro_tbel_4076, retro_tbel_4138, retro_tbel_4462, retro_tbel_4711, retro_tbel_720,
Tarsius syrichta ENSTSYG000000012711 retrocopy
retro_tsyr_677,


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