RetrogeneDB ID:

retro_opri_900

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_4269:56253..56709(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL24
Ensembl ID:ENSOPRG00000004255
Aliases:None
Description:ribosomal protein L24 [Source:HGNC Symbol;Acc:10325]


Retrocopy-Parental alignment summary:






>retro_opri_900
TCCCTTCGCCATCTTTCCTCTTCCAGGGGAGCCGCCGCCATGAAGATTGAATTCTGCAGTTTCAGTGGGCACAAGATCTA
TCCCGGACACGGGGAGACGCTACGCCAGAACCGACGGGAAGGTTTTCCAGTTTCTTAACGCAAAATGCGAGTTTGCGTTT
CTTTCCAAGAGGAATCTGCAGCAGATCAGTTGGGCTGTCCTCTACTGAAGGAAACACAAAAAGGGGCAGTCAGAAGAAAT
TCAAAAGAAAAGAACTCGTCGTGCAAATTCTAGAGAGCCGTCATTGGTGCGCCTCTTGCTGATACCGTGGCCAAGAGAAA
TCAGAAGCCTGAAGTTAGGAAGGCTCAACGAGAACAAGCGGTCAGCGCTGCCAAGGAAGCCAAACAGGCTACGCAGACGT
CTAAAAAGACAGCAATGCCTGCTGCTAAGGCTCTTGCAAAAGCAGCGCCTAAGCAA

ORF - retro_opri_900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.35 %
Parental protein coverage: 88.44 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSLRHLSSSRGAAAMKVELCSFSGYKIYPGHG-RRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYR
SLRHLSSSRGAAAMK.E.CSFSG.KIYPGHG.RRYARTDGKVFQFLNAKCE.AFLSKRN..QI.W.VLY.
RetrocopySLRHLSSSRGAAAMKIEFCSFSGHKIYPGHG>RRYARTDGKVFQFLNAKCEFAFLSKRNLQQISWAVLY*
ParentalRKHKKGQSEEIQKKRTRR-AVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKT
RKHKKGQSEEI..K...R...KF.RA..GA.LAD..AKRNQKPEVRKAQREQA..AAKEAK.A.Q.SKKT
RetrocopyRKHKKGQSEEI-QKKRTR<SCKF*RAVIGAPLADTVAKRNQKPEVRKAQREQAVSAAKEAKQATQTSKKT
ParentalAMAAAKAPTKAAPKQ
AM.AAKA..KAAPKQ
RetrocopyAMPAAKALAKAAPKQ

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_900 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 25 parental genes, and 162 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000134611 retrocopy
retro_btau_1143,
Callithrix jacchus ENSCJAG000000004963 retrocopies
retro_cjac_2544, retro_cjac_2941, retro_cjac_327,
Cavia porcellus ENSCPOG000000199415 retrocopies
retro_cpor_1020, retro_cpor_461, retro_cpor_474, retro_cpor_904, retro_cpor_947,
Dasypus novemcinctus ENSDNOG000000031949 retrocopies
retro_dnov_1209, retro_dnov_1259, retro_dnov_1449, retro_dnov_1643, retro_dnov_2191, retro_dnov_2407, retro_dnov_2537, retro_dnov_523, retro_dnov_657,
Erinaceus europaeus ENSEEUG000000093203 retrocopies
retro_eeur_505, retro_eeur_534, retro_eeur_621,
Felis catus ENSFCAG000000033271 retrocopy
retro_fcat_31,
Homo sapiens ENSG000001143918 retrocopies
retro_hsap_1437, retro_hsap_1752, retro_hsap_2418, retro_hsap_2614, retro_hsap_2743, retro_hsap_281, retro_hsap_3583, retro_hsap_4179,
Gorilla gorilla ENSGGOG000000116098 retrocopies
retro_ggor_1106, retro_ggor_1504, retro_ggor_1831, retro_ggor_1909, retro_ggor_2252, retro_ggor_2417, retro_ggor_2803, retro_ggor_324,
Macropus eugenii ENSMEUG000000091777 retrocopies
retro_meug_1769, retro_meug_371, retro_meug_385, retro_meug_449, retro_meug_730, retro_meug_759, retro_meug_963,
Myotis lucifugus ENSMLUG000000170054 retrocopies
retro_mluc_1990, retro_mluc_2185, retro_mluc_35, retro_mluc_393,
Macaca mulatta ENSMMUG000000150599 retrocopies
retro_mmul_1234, retro_mmul_1711, retro_mmul_1803, retro_mmul_2263, retro_mmul_2521, retro_mmul_37, retro_mmul_560, retro_mmul_609, retro_mmul_823,
Monodelphis domestica ENSMODG000000019163 retrocopies
retro_mdom_675, retro_mdom_854, retro_mdom_974,
Nomascus leucogenys ENSNLEG000000032766 retrocopies
retro_nleu_1413, retro_nleu_1790, retro_nleu_1894, retro_nleu_2031, retro_nleu_2815, retro_nleu_2937,
Oryctolagus cuniculus ENSOCUG000000007918 retrocopies
retro_ocun_1401, retro_ocun_190, retro_ocun_303, retro_ocun_323, retro_ocun_420, retro_ocun_480, retro_ocun_526, retro_ocun_531,
Ochotona princeps ENSOPRG00000004255 6 retrocopies
retro_opri_1100, retro_opri_1109, retro_opri_1131, retro_opri_900 , retro_opri_918, retro_opri_95,
Procavia capensis ENSPCAG000000059181 retrocopy
retro_pcap_192,
Pongo abelii ENSPPYG000000135886 retrocopies
retro_pabe_1191, retro_pabe_1450, retro_pabe_1782, retro_pabe_2277, retro_pabe_2343, retro_pabe_3419,
Pan troglodytes ENSPTRG000000151762 retrocopies
retro_ptro_1214, retro_ptro_85,
Pteropus vampyrus ENSPVAG000000098893 retrocopies
retro_pvam_1317, retro_pvam_743, retro_pvam_831,
Rattus norvegicus ENSRNOG0000000161125 retrocopies
retro_rnor_1244, retro_rnor_1245, retro_rnor_1247, retro_rnor_1248, retro_rnor_1250, retro_rnor_1251, retro_rnor_1252, retro_rnor_1253, retro_rnor_1452, retro_rnor_1643, retro_rnor_1699, retro_rnor_1850, retro_rnor_1851, retro_rnor_1985, retro_rnor_2026, retro_rnor_2134, retro_rnor_2148, retro_rnor_2205, retro_rnor_2214, retro_rnor_2294, retro_rnor_2709, retro_rnor_435, retro_rnor_751, retro_rnor_964, retro_rnor_993,
Sorex araneus ENSSARG000000076156 retrocopies
retro_sara_198, retro_sara_204, retro_sara_330, retro_sara_535, retro_sara_574, retro_sara_711,
Sarcophilus harrisii ENSSHAG000000082262 retrocopies
retro_shar_171, retro_shar_264,
Ictidomys tridecemlineatus ENSSTOG000000146542 retrocopies
retro_itri_442, retro_itri_69,
Tupaia belangeri ENSTBEG0000001204430 retrocopies
retro_tbel_1349, retro_tbel_1429, retro_tbel_1676, retro_tbel_2076, retro_tbel_2248, retro_tbel_2553, retro_tbel_2836, retro_tbel_2853, retro_tbel_2931, retro_tbel_3363, retro_tbel_3507, retro_tbel_3544, retro_tbel_3552, retro_tbel_3557, retro_tbel_3634, retro_tbel_3636, retro_tbel_3664, retro_tbel_4105, retro_tbel_4114, retro_tbel_4139, retro_tbel_4236, retro_tbel_4237, retro_tbel_431, retro_tbel_4677, retro_tbel_569, retro_tbel_607, retro_tbel_678, retro_tbel_700, retro_tbel_73, retro_tbel_779,
Tarsius syrichta ENSTSYG000000023144 retrocopies
retro_tsyr_266, retro_tsyr_285, retro_tsyr_401, retro_tsyr_460,


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