RetrogeneDB ID:

retro_amel_342

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192393.1:551918..552366(+)
Located in intron of:ENSAMEG00000012095
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5G2
Ensembl ID:ENSAMEG00000000619
Aliases:None
Description:ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9) [Source:HGNC Symbol;Acc:842]


Retrocopy-Parental alignment summary:






>retro_amel_342
GCCACAGCCAGTCGTCCCCTAAAAATGGACGCCAGGTGCAAAGTTCGTCTCCACCCCCTTCTTGGTGAGGAGCACCTCTC
CGCTGTTGAGTTGAACACCGTCTGCAGTGGTGCTAAAACCACTGGAGACACTGACAGATGACAGTCTCAGCAGCTCGGCA
GCCCCACGTACCCTGACCTCACTTACTCCCACCCGCAGCTTCTGAACCAGCACCATTTCAAGGGACATCCACACAACGGC
CAAGTTCACTGGGGCTGGGGCTGCCACGGTAGGGGGGGGGCTGGCTCTGGGGCTGGAATTGGGACTGTGTTTGGGAGTCT
CCTCATTGGTTATGCCACGAACCCCTCTCTGAAGCAAAGGCTGTTCTCCTAACTCCATTCTGGGCTCTGCCCTCTTCGAG
GCCCTACAGCTCTTTTGCCTGATGGCGGTCTTTCTCATCCTCTTTGCC

ORF - retro_amel_342 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.08 %
Parental protein coverage: 75.13 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalATAPHPLKMYAC-AKFVSTPFLAKSTSQLLSRSLSAVVLKPPETLTDESLSSLAAPRPLTSLIPSRSFQT
ATA..PLKM.A..AKFVSTPFL..STS.LLS...SAVVLKP.ETLTD.SLSS.AAPR.LTSL.P.RSF.T
RetrocopyATASRPLKMDAR>AKFVSTPFLVRSTSPLLS*TPSAVVLKPLETLTDDSLSSSAAPRTLTSLTPTRSF*T
ParentalSAISRDIDTAAKFIGAGAATV-GVAGSGAGIGTVFG-SLIIGYARNPSLKQQLFS-YAILGFALSEAMGL
S.ISRDI.T.AKF.GAGAATV......G...G...G.SL.IGYA.NPSLKQ.LFS...ILG.AL.EA..L
RetrocopySTISRDIHTTAKFTGAGAATVXXXLALGLELGLCLG<SLLIGYATNPSLKQRLFS>NSILGSALFEALQL
ParentalFCLMVAFLILFA
FCLM..FLILFA
RetrocopyFCLMAVFLILFA

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






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_342 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_342 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca 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 252 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000000619 18 retrocopies
retro_amel_1077, retro_amel_1113, retro_amel_1166, retro_amel_1309, retro_amel_1317, retro_amel_1322, retro_amel_1323, retro_amel_1610, retro_amel_1851, retro_amel_209, retro_amel_227, retro_amel_244, retro_amel_342 , retro_amel_363, retro_amel_578, retro_amel_632, retro_amel_770, retro_amel_919,
Ailuropoda melanoleuca ENSAMEG000000123671 retrocopy
retro_amel_1829,
Bos taurus ENSBTAG0000000573511 retrocopies
retro_btau_1405, retro_btau_1414, retro_btau_733, retro_btau_734, retro_btau_735, retro_btau_737, retro_btau_739, retro_btau_740, retro_btau_741, retro_btau_742, retro_btau_994,
Cavia porcellus ENSCPOG000000228893 retrocopies
retro_cpor_1495, retro_cpor_268, retro_cpor_492,
Equus caballus ENSECAG000000230212 retrocopies
retro_ecab_373, retro_ecab_793,
Erinaceus europaeus ENSEEUG000000030511 retrocopy
retro_eeur_79,
Echinops telfairi ENSETEG0000000596840 retrocopies
retro_etel_1001, retro_etel_1007, retro_etel_103, retro_etel_1191, retro_etel_1203, retro_etel_1259, retro_etel_1288, retro_etel_1301, retro_etel_1327, retro_etel_1332, retro_etel_1354, retro_etel_1374, retro_etel_1402, retro_etel_1404, retro_etel_1420, retro_etel_1427, retro_etel_144, retro_etel_1533, retro_etel_1535, retro_etel_1591, retro_etel_1662, retro_etel_1684, retro_etel_1712, retro_etel_1771, retro_etel_2011, retro_etel_2127, retro_etel_2128, retro_etel_2142, retro_etel_2207, retro_etel_2216, retro_etel_260, retro_etel_475, retro_etel_636, retro_etel_639, retro_etel_652, retro_etel_72, retro_etel_735, retro_etel_736, retro_etel_796, retro_etel_847,
Felis catus ENSFCAG0000000150213 retrocopies
retro_fcat_1126, retro_fcat_1345, retro_fcat_1611, retro_fcat_1785, retro_fcat_1952, retro_fcat_226, retro_fcat_351, retro_fcat_353, retro_fcat_363, retro_fcat_405, retro_fcat_668, retro_fcat_958, retro_fcat_999,
Homo sapiens ENSG000001353906 retrocopies
retro_hsap_1332, retro_hsap_2195, retro_hsap_2703, retro_hsap_3782, retro_hsap_4813, retro_hsap_499,
Gorilla gorilla ENSGGOG000000156415 retrocopies
retro_ggor_1039, retro_ggor_1737, retro_ggor_1884, retro_ggor_2543, retro_ggor_2999,
Macropus eugenii ENSMEUG0000000466167 retrocopies
retro_meug_1009, retro_meug_1030, retro_meug_113, retro_meug_1180, retro_meug_1187, retro_meug_1238, retro_meug_1258, retro_meug_1261, retro_meug_1265, retro_meug_1272, retro_meug_1284, retro_meug_1297, retro_meug_1322, retro_meug_1328, retro_meug_1361, retro_meug_1389, retro_meug_1413, retro_meug_1602, retro_meug_1626, retro_meug_1639, retro_meug_1653, retro_meug_1709, retro_meug_1752, retro_meug_177, retro_meug_1802, retro_meug_1843, retro_meug_1882, retro_meug_1885, retro_meug_1891, retro_meug_1903, retro_meug_1909, retro_meug_1919, retro_meug_193, retro_meug_1987, retro_meug_2014, retro_meug_2048, retro_meug_206, retro_meug_2073, retro_meug_2111, retro_meug_2115, retro_meug_2122, retro_meug_216, retro_meug_229, retro_meug_230, retro_meug_296, retro_meug_313, retro_meug_345, retro_meug_348, retro_meug_397, retro_meug_485, retro_meug_514, retro_meug_529, retro_meug_567, retro_meug_622, retro_meug_66, retro_meug_721, retro_meug_742, retro_meug_799, retro_meug_800, retro_meug_846, retro_meug_864, retro_meug_865, retro_meug_896, retro_meug_904, retro_meug_935, retro_meug_936, retro_meug_983,
Microcebus murinus ENSMICG000000116864 retrocopies
retro_mmur_175, retro_mmur_373, retro_mmur_905, retro_mmur_977,
Myotis lucifugus ENSMLUG0000001186013 retrocopies
retro_mluc_106, retro_mluc_1215, retro_mluc_1335, retro_mluc_1337, retro_mluc_1496, retro_mluc_1633, retro_mluc_2151, retro_mluc_2186, retro_mluc_2257, retro_mluc_2273, retro_mluc_516, retro_mluc_575, retro_mluc_656,
Macaca mulatta ENSMMUG000000162413 retrocopies
retro_mmul_1539, retro_mmul_2173, retro_mmul_439,
Mustela putorius furoENSMPUG000000059276 retrocopies
retro_mputfur_1650, retro_mputfur_290, retro_mputfur_335, retro_mputfur_631, retro_mputfur_814, retro_mputfur_947,
Mus musculus ENSMUSG000000626831 retrocopy
retro_mmus_6,
Nomascus leucogenys ENSNLEG000000176864 retrocopies
retro_nleu_1576, retro_nleu_2187, retro_nleu_2403, retro_nleu_326,
Oryctolagus cuniculus ENSOCUG000000089334 retrocopies
retro_ocun_1933, retro_ocun_450, retro_ocun_762, retro_ocun_794,
Otolemur garnettii ENSOGAG000000036114 retrocopies
retro_ogar_142, retro_ogar_1620, retro_ogar_166, retro_ogar_2415,
Ochotona princeps ENSOPRG000000029781 retrocopy
retro_opri_671,
Procavia capensis ENSPCAG000000086793 retrocopies
retro_pcap_140, retro_pcap_189, retro_pcap_212,
Pongo abelii ENSPPYG000000045867 retrocopies
retro_pabe_1211, retro_pabe_1212, retro_pabe_2073, retro_pabe_2255, retro_pabe_236, retro_pabe_3088, retro_pabe_3741,
Pan troglodytes ENSPTRG000000050236 retrocopies
retro_ptro_1668, retro_ptro_1824, retro_ptro_2563, retro_ptro_3202, retro_ptro_376, retro_ptro_909,
Pteropus vampyrus ENSPVAG000000122911 retrocopy
retro_pvam_146,
Rattus norvegicus ENSRNOG000000153206 retrocopies
retro_rnor_1286, retro_rnor_1490, retro_rnor_1939, retro_rnor_2699, retro_rnor_2738, retro_rnor_2910,
Sorex araneus ENSSARG000000010277 retrocopies
retro_sara_124, retro_sara_152, retro_sara_377, retro_sara_581, retro_sara_716, retro_sara_73, retro_sara_759,
Sarcophilus harrisii ENSSHAG000000057264 retrocopies
retro_shar_163, retro_shar_417, retro_shar_653, retro_shar_678,
Ictidomys tridecemlineatus ENSSTOG000000082173 retrocopies
retro_itri_1404, retro_itri_399, retro_itri_436,
Tupaia belangeri ENSTBEG000000057484 retrocopies
retro_tbel_1358, retro_tbel_1467, retro_tbel_2095, retro_tbel_789,
Tarsius syrichta ENSTSYG000000034334 retrocopies
retro_tsyr_147, retro_tsyr_795, retro_tsyr_876, retro_tsyr_915,


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