RetrogeneDB ID:

retro_opri_159

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_3016:508630..509140(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSOPRG00000011713
Aliases:None
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_opri_159
AAAAAACTGGAAAAGCAACAGAATGGAAAGAGTAAAAAGGTCAAAGAGGCAGAGCCTGAAGAATTTGTGGTGGAGAATAT
GTTGGACCAACATGTGGTCCAGGGAGGGTGGAGTACTGCCTCAAGTGGGAAGGATTTACAGATGCTGACAACACTTGGGA
ACCTGAAGGACATTTAGATCATCCAGAGTTAATGGAAGAATTTCTTGATTCTCAAAAAGCTGGTAAAGAAAACGATGGTA
CAAAAAGAAAATTTTCTCTGACAGTGACTTTGATGACAGTCAATCAAAGCAGAAGAGATGCTGCTGAGAAACCCAGAGGC
TCAGCCAGGGCTCCTGGTCGCAGCCGGTCACTGGCGCCACAGACAGCACTGCACAACTCATGCTCCTCATGAAATGCAGA
CATTCAGATGGGGCTGACTGGGTGCTGGCCAAAGAAGCAACAACGAAATGTCTCCGATTGTAACTGCTTTTTATGAAGAG
ACTAAGTGGCATTCCTGTCCGGAAGACAAG

ORF - retro_opri_159 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.07 %
Parental protein coverage: 98.86 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVN-GKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFL
.K..K.QNGKSKKV.EAEPEEFVVE..LD..VV..G.VEY.LKW.GFTDADNTWEPE..LD.PEL.E.FL
RetrocopyKKLEKQQNGKSKKVKEAEPEEFVVENMLDQHVVQ<GRVEYCLKWEGFTDADNTWEPEGHLDHPELMEEFL
ParentalNSQKAGKEKDGAKR-KSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSD
.SQKAGKE.DG.KR.K..SDS..DDS.SK.KR......R....G.......GATDS...LM.LMK...SD
RetrocopyDSQKAGKENDGTKR<KIFSDSDFDDSQSKQKRCC*ETQR-LSQGSWSQPVTGATDSTAQLMLLMKCRHSD
ParentalEADLVLAKEANMKC-PQIVIAFYEERLTWHSCPEDE
.AD.VLAKEA..KC...IV.AFYEE...WHSCPED.
RetrocopyGADWVLAKEATTKC<SPIVTAFYEE-TKWHSCPEDK

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_159 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 30 parental genes, and 182 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000059691 retrocopy
retro_amel_1184,
Canis familiaris ENSCAFG0000000289711 retrocopies
retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Choloepus hoffmanni ENSCHOG0000001384322 retrocopies
retro_chof_1128, retro_chof_1147, retro_chof_1156, retro_chof_1178, retro_chof_1210, retro_chof_1223, retro_chof_132, retro_chof_1569, retro_chof_1672, retro_chof_1779, retro_chof_1863, retro_chof_1962, retro_chof_222, retro_chof_2269, retro_chof_2347, retro_chof_2379, retro_chof_2435, retro_chof_2695, retro_chof_411, retro_chof_676, retro_chof_87, retro_chof_936,
Callithrix jacchus ENSCJAG000000079528 retrocopies
retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Cavia porcellus ENSCPOG000000151681 retrocopy
retro_cpor_66,
Dasypus novemcinctus ENSDNOG0000000625019 retrocopies
retro_dnov_1136, retro_dnov_1174, retro_dnov_1208, retro_dnov_1270, retro_dnov_1605, retro_dnov_2306, retro_dnov_2307, retro_dnov_2397, retro_dnov_2543, retro_dnov_2605, retro_dnov_2633, retro_dnov_321, retro_dnov_359, retro_dnov_385, retro_dnov_445, retro_dnov_772, retro_dnov_794, retro_dnov_833, retro_dnov_844,
Dipodomys ordii ENSDORG0000000548711 retrocopies
retro_dord_309, retro_dord_405, retro_dord_437, retro_dord_440, retro_dord_456, retro_dord_502, retro_dord_629, retro_dord_630, retro_dord_655, retro_dord_700, retro_dord_780,
Equus caballus ENSECAG000000127801 retrocopy
retro_ecab_784,
Felis catus ENSFCAG000000152246 retrocopies
retro_fcat_1005, retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Homo sapiens ENSG000001225659 retrocopies
retro_hsap_1071, retro_hsap_1145, retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Gorilla gorilla ENSGGOG000000258536 retrocopies
retro_ggor_1928, retro_ggor_2281, retro_ggor_2466, retro_ggor_2467, retro_ggor_635, retro_ggor_845,
Loxodonta africana ENSLAFG000000069073 retrocopies
retro_lafr_661, retro_lafr_687, retro_lafr_776,
Microcebus murinus ENSMICG0000000699811 retrocopies
retro_mmur_1015, retro_mmur_1030, retro_mmur_1076, retro_mmur_1178, retro_mmur_1497, retro_mmur_1500, retro_mmur_1548, retro_mmur_386, retro_mmur_421, retro_mmur_68, retro_mmur_685,
Myotis lucifugus ENSMLUG000000075912 retrocopies
retro_mluc_2486, retro_mluc_813,
Mus musculus ENSMUSG000000298361 retrocopy
retro_mmus_77,
Nomascus leucogenys ENSNLEG000000149319 retrocopies
retro_nleu_141, retro_nleu_1685, retro_nleu_2462, retro_nleu_373, retro_nleu_397, retro_nleu_511, retro_nleu_676, retro_nleu_944, retro_nleu_964,
Otolemur garnettii ENSOGAG000000165831 retrocopy
retro_ogar_136,
Ochotona princeps ENSOPRG000000036991 retrocopy
retro_opri_552,
Ochotona princeps ENSOPRG00000011713 9 retrocopies
retro_opri_103, retro_opri_159 , retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Procavia capensis ENSPCAG000000049042 retrocopies
retro_pcap_108, retro_pcap_166,
Pongo abelii ENSPPYG0000001771410 retrocopies
retro_pabe_2112, retro_pabe_2243, retro_pabe_2724, retro_pabe_2770, retro_pabe_2997, retro_pabe_3608, retro_pabe_758, retro_pabe_786, retro_pabe_892, retro_pabe_951,
Pan troglodytes ENSPTRG0000001900310 retrocopies
retro_ptro_17, retro_ptro_1706, retro_ptro_1875, retro_ptro_2289, retro_ptro_2475, retro_ptro_395, retro_ptro_537, retro_ptro_630, retro_ptro_729, retro_ptro_780,
Pteropus vampyrus ENSPVAG000000062972 retrocopies
retro_pvam_294, retro_pvam_786,
Rattus norvegicus ENSRNOG000000118142 retrocopies
retro_rnor_120, retro_rnor_301,
Sorex araneus ENSSARG000000080112 retrocopies
retro_sara_496, retro_sara_709,
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
retro_shar_153,
Sus scrofa ENSSSCG000000167114 retrocopies
retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,
Ictidomys tridecemlineatus ENSSTOG000000062234 retrocopies
retro_itri_1093, retro_itri_1682, retro_itri_1764, retro_itri_912,
Tarsius syrichta ENSTSYG000000081596 retrocopies
retro_tsyr_1459, retro_tsyr_1545, retro_tsyr_1552, retro_tsyr_1645, retro_tsyr_203, retro_tsyr_583,
Tursiops truncatus ENSTTRG000000007117 retrocopies
retro_ttru_1238, retro_ttru_1247, retro_ttru_1851, retro_ttru_294, retro_ttru_52, retro_ttru_591, retro_ttru_644,


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