RetrogeneDB ID:

retro_lafr_916

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_5:11954615..11955008(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACP1
Ensembl ID:ENSLAFG00000002966
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_916
AGGTCTGTGCTGTTTGTATGTCTGGGTAAGATTTGTCAATCACTCATTGCAGAAGCAGTTTTCAGAAAATTTGCAACTGA
TCAAAATCTTTTAGACAAGACAGTGCAACAGCACCCACATATGAAATAGGAAACCCTCCTGATTGTCGAGGGCAAAACTG
CGTGAAGAAGCATGCCATTCCTATGAATCACATCGCCCGGCAGGTTACCCAGAAGACTTTGCACGTTTGATTATACACTG
TGTATGGATGGAAGCAATCTGAGAGATCTGAATAGAACAGGTAATCAAGTTAAATATTGCAAAGCTAAAATTGAACTACT
TGGAAGCTATGATCCATAAAAATGACTTATTATTGAAGATCTCTATTATGGGAAGGACACCGACTTTGAGACC

ORF - retro_lafr_916 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.91 %
Parental protein coverage: 85.44 %
Number of stop codons detected: 3
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalKSVLFVCLGNICRSPIAEAV-FRKLVADQNLLDKWRIDSAATSTYEIGNPPDYRGQNCMKKHGIPMNHIA
.SVLFVCLG.IC.S.IAEAV.F.K.....N.....R.DSA...TYEIGNPPD.RGQNC.KKH.IPMNHIA
RetrocopyRSVLFVCLGKICQSLIAEAV<FQKIC---N*SKSFRQDSATAPTYEIGNPPDCRGQNCVKKHAIPMNHIA
ParentalRQVTR-EDFA-TFDYILCMDESNLRDLNRKGNQVKNCKAKIELLGSYDPQKQLVIEDPYYGNDSDFET
RQVT..EDFA.TFDY.LCMD.SNLRDLNR.GNQVK.CKAKIELLGSYDP.K.L.IED.YYG.D.DFET
RetrocopyRQVTQ<EDFA<TFDYTLCMDGSNLRDLNRTGNQVKYCKAKIELLGSYDP*K*LIIEDLYYGKDTDFET

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






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_916 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana 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 33 parental genes, and 276 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095542 retrocopies
retro_amel_705, retro_amel_761,
Bos taurus ENSBTAG000000204984 retrocopies
retro_btau_1085, retro_btau_1099, retro_btau_1695, retro_btau_421,
Canis familiaris ENSCAFG000000300971 retrocopy
retro_cfam_1126,
Choloepus hoffmanni ENSCHOG0000000389194 retrocopies
retro_chof_1010, retro_chof_1053, retro_chof_1073, retro_chof_1099, retro_chof_1100, retro_chof_1144, retro_chof_119, retro_chof_1190, retro_chof_121, retro_chof_1259, retro_chof_1265, retro_chof_1275, retro_chof_1330, retro_chof_1351, retro_chof_1359, retro_chof_1389, retro_chof_1390, retro_chof_1412, retro_chof_142, retro_chof_1444, retro_chof_1447, retro_chof_1508, retro_chof_1567, retro_chof_1570, retro_chof_1593, retro_chof_1632, retro_chof_1633, retro_chof_1658, retro_chof_1684, retro_chof_169, retro_chof_1698, retro_chof_17, retro_chof_1716, retro_chof_174, retro_chof_1799, retro_chof_1802, retro_chof_1815, retro_chof_1833, retro_chof_1838, retro_chof_1864, retro_chof_1941, retro_chof_1956, retro_chof_1993, retro_chof_2012, retro_chof_2041, retro_chof_2044, retro_chof_2091, retro_chof_2165, retro_chof_2192, retro_chof_2208, retro_chof_2228, retro_chof_2259, retro_chof_2344, retro_chof_2378, retro_chof_2384, retro_chof_2443, retro_chof_245, retro_chof_2478, retro_chof_2512, retro_chof_2532, retro_chof_2542, retro_chof_2551, retro_chof_261, retro_chof_262, retro_chof_2622, retro_chof_2636, retro_chof_2643, retro_chof_2653, retro_chof_2654, retro_chof_2678, retro_chof_2701, retro_chof_2705, retro_chof_2707, retro_chof_319, retro_chof_377, retro_chof_460, retro_chof_598, retro_chof_603, retro_chof_649, retro_chof_650, retro_chof_66, retro_chof_727, retro_chof_80, retro_chof_803, retro_chof_83, retro_chof_842, retro_chof_934, retro_chof_939, retro_chof_958, retro_chof_962, retro_chof_986, retro_chof_991, retro_chof_994, retro_chof_999,
Callithrix jacchus ENSCJAG000000116635 retrocopies
retro_cjac_1226, retro_cjac_2082, retro_cjac_2162, retro_cjac_405, retro_cjac_609,
Cavia porcellus ENSCPOG000000028624 retrocopies
retro_cpor_215, retro_cpor_614, retro_cpor_678, retro_cpor_868,
Dasypus novemcinctus ENSDNOG0000001738232 retrocopies
retro_dnov_1166, retro_dnov_1213, retro_dnov_1234, retro_dnov_1255, retro_dnov_1302, retro_dnov_136, retro_dnov_1373, retro_dnov_1393, retro_dnov_1499, retro_dnov_1553, retro_dnov_1601, retro_dnov_1685, retro_dnov_1709, retro_dnov_1732, retro_dnov_1895, retro_dnov_1937, retro_dnov_1950, retro_dnov_2320, retro_dnov_2349, retro_dnov_2509, retro_dnov_2582, retro_dnov_297, retro_dnov_312, retro_dnov_355, retro_dnov_474, retro_dnov_501, retro_dnov_535, retro_dnov_650, retro_dnov_768, retro_dnov_81, retro_dnov_830, retro_dnov_987,
Dipodomys ordii ENSDORG000000164696 retrocopies
retro_dord_112, retro_dord_156, retro_dord_383, retro_dord_410, retro_dord_541, retro_dord_55,
Equus caballus ENSECAG000000100791 retrocopy
retro_ecab_135,
Erinaceus europaeus ENSEEUG000000154681 retrocopy
retro_eeur_574,
Echinops telfairi ENSETEG0000001376418 retrocopies
retro_etel_100, retro_etel_1034, retro_etel_110, retro_etel_1204, retro_etel_1655, retro_etel_1718, retro_etel_1824, retro_etel_1861, retro_etel_1940, retro_etel_2133, retro_etel_230, retro_etel_343, retro_etel_398, retro_etel_420, retro_etel_679, retro_etel_797, retro_etel_82, retro_etel_958,
Felis catus ENSFCAG000000267171 retrocopy
retro_fcat_1472,
Homo sapiens ENSG000001437275 retrocopies
retro_hsap_1627, retro_hsap_1666, retro_hsap_1667, retro_hsap_529, retro_hsap_603,
Gorilla gorilla ENSGGOG000000155775 retrocopies
retro_ggor_1228, retro_ggor_1256, retro_ggor_485, retro_ggor_532, retro_ggor_72,
Loxodonta africana ENSLAFG00000002966 4 retrocopies
retro_lafr_1053, retro_lafr_1227, retro_lafr_336, retro_lafr_916 ,
Macropus eugenii ENSMEUG000000107333 retrocopies
retro_meug_1736, retro_meug_706, retro_meug_806,
Myotis lucifugus ENSMLUG000000177074 retrocopies
retro_mluc_133, retro_mluc_1970, retro_mluc_548, retro_mluc_686,
Macaca mulatta ENSMMUG000000170972 retrocopies
retro_mmul_1575, retro_mmul_2447,
Monodelphis domestica ENSMODG000000257643 retrocopies
retro_mdom_236, retro_mdom_292, retro_mdom_364,
Mustela putorius furoENSMPUG000000127872 retrocopies
retro_mputfur_1420, retro_mputfur_1619,
Mus musculus ENSMUSG0000004457311 retrocopies
retro_mmus_1041, retro_mmus_1103, retro_mmus_1230, retro_mmus_1261, retro_mmus_2133, retro_mmus_2143, retro_mmus_2155, retro_mmus_2969, retro_mmus_3690, retro_mmus_455, retro_mmus_717,
Nomascus leucogenys ENSNLEG000000083596 retrocopies
retro_nleu_1784, retro_nleu_2230, retro_nleu_2683, retro_nleu_2792, retro_nleu_2821, retro_nleu_2915,
Oryctolagus cuniculus ENSOCUG0000001287611 retrocopies
retro_ocun_1192, retro_ocun_1302, retro_ocun_1328, retro_ocun_1347, retro_ocun_1358, retro_ocun_1501, retro_ocun_1610, retro_ocun_1743, retro_ocun_1744, retro_ocun_1859, retro_ocun_1860,
Otolemur garnettii ENSOGAG000000003015 retrocopies
retro_ogar_1665, retro_ogar_2357, retro_ogar_3182, retro_ogar_426, retro_ogar_471,
Procavia capensis ENSPCAG000000120541 retrocopy
retro_pcap_312,
Pongo abelii ENSPPYG000000126946 retrocopies
retro_pabe_1374, retro_pabe_1406, retro_pabe_1748, retro_pabe_220, retro_pabe_543, retro_pabe_588,
Pan troglodytes ENSPTRG000000116055 retrocopies
retro_ptro_1129, retro_ptro_2959, retro_ptro_3050, retro_ptro_3080, retro_ptro_446,
Pteropus vampyrus ENSPVAG000000133875 retrocopies
retro_pvam_1117, retro_pvam_1401, retro_pvam_28, retro_pvam_781, retro_pvam_944,
Rattus norvegicus ENSRNOG0000000526011 retrocopies
retro_rnor_1201, retro_rnor_1302, retro_rnor_1303, retro_rnor_1476, retro_rnor_1802, retro_rnor_2079, retro_rnor_2382, retro_rnor_2569, retro_rnor_2772, retro_rnor_449, retro_rnor_457,
Sarcophilus harrisii ENSSHAG000000052164 retrocopies
retro_shar_306, retro_shar_529, retro_shar_655, retro_shar_772,
Ictidomys tridecemlineatus ENSSTOG000000025203 retrocopies
retro_itri_1010, retro_itri_1581, retro_itri_821,
Tarsius syrichta ENSTSYG000000048647 retrocopies
retro_tsyr_1013, retro_tsyr_1214, retro_tsyr_1477, retro_tsyr_1482, retro_tsyr_209, retro_tsyr_444, retro_tsyr_523,
Tursiops truncatus ENSTTRG000000107704 retrocopies
retro_ttru_130, retro_ttru_1934, retro_ttru_293, retro_ttru_392,


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