RetrogeneDB ID:

retro_shar_334

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL841374.1:72123..72501(-)
Located in intron of:ENSSHAG00000000912
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000000731
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_334
ATGCTGATGCCAAGAAGAACTAAGTTGTCATCTATGAACTCCTTTTGAAGGAGAGAGTAATGGTAGACAAGAAGGATGTC
CATGTGCCAAAGCGCCCTGAGCTGGCAGACAAGAATGTGTCCAGACTCCATGTCATGAAAGCCAGGCATTCTTGTAATGT
CTCCTGGCTATGTTACGGAGCAGTTTGCATGGAGGCATTTCTCTTGGTACCTAACCAATGAAGCTATTCATGCTTCAGGG
ATTACCTTCACCTCCTCCTAAGATTGTGTTTGCCACCCTATACAGAAGTCCTGAGACAGGAGGGAGCAAAGTCCTGGCCT
GGAGGGTGGGCATTCTTCCTGGCTTACTCAGGGTGAACCTGACAGAGACACTTACAAA

ORF - retro_shar_334 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.42 %
Parental protein coverage: 77.58 %
Number of stop codons detected: 1
Number of frameshifts detected: 5


Retrocopy - Parental Gene Alignment:

ParentalMLMP-KKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQS-LKSRGYVKEQFAWRHFY
MLMP.KKN...IYELL.KE.VMV.KKDVH.PK.PELADKNV..LHVMKA..S...S.GYV.EQFAWRHF.
RetrocopyMLMP<KKN*VVIYELLLKERVMVDKKDVHVPKRPELADKNVSRLHVMKARHS>VMSPGYVTEQFAWRHFS
ParentalWYLTNEGI-QYLRDYLHL-PPEIVPATLRRSRPETG-RPRPKGLEGERPARLTRGEADRDTYR
WYLTNE.I....RDYLHL.PP.IV.ATL.RS.PETG.R....GLEG.....LT.GE.DRDTY.
RetrocopyWYLTNEAI<SCFRDYLHL<PPKIVFATLYRS-PETG<REQSPGLEGGHSSWLTQGEPDRDTYK

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






RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_334 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii 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 165 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000010474 retrocopies
retro_amel_1408, retro_amel_1706, retro_amel_446, retro_amel_890,
Bos taurus ENSBTAG000000155983 retrocopies
retro_btau_1334, retro_btau_844, retro_btau_989,
Canis familiaris ENSCAFG000000012142 retrocopies
retro_cfam_1, retro_cfam_92,
Callithrix jacchus ENSCJAG000000152504 retrocopies
retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Cavia porcellus ENSCPOG000000086132 retrocopies
retro_cpor_1245, retro_cpor_345,
Dasypus novemcinctus ENSDNOG000000116702 retrocopies
retro_dnov_2303, retro_dnov_2558,
Dipodomys ordii ENSDORG000000120606 retrocopies
retro_dord_225, retro_dord_494, retro_dord_641, retro_dord_73, retro_dord_74, retro_dord_767,
Equus caballus ENSECAG000000064301 retrocopy
retro_ecab_198,
Erinaceus europaeus ENSEEUG000000033762 retrocopies
retro_eeur_367, retro_eeur_647,
Felis catus ENSFCAG000000153553 retrocopies
retro_fcat_1443, retro_fcat_1681, retro_fcat_1757,
Homo sapiens ENSG0000012461424 retrocopies
retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289, retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454, retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae ENSLACG000000172191 retrocopy
retro_lcha_26,
Loxodonta africana ENSLAFG000000085391 retrocopy
retro_lafr_756,
Myotis lucifugus ENSMLUG000000074952 retrocopies
retro_mluc_1143, retro_mluc_2128,
Macaca mulatta ENSMMUG000000002672 retrocopies
retro_mmul_332, retro_mmul_555,
Monodelphis domestica ENSMODG000000139292 retrocopies
retro_mdom_1889, retro_mdom_437,
Mustela putorius furoENSMPUG000000031173 retrocopies
retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus ENSMUSG000000521469 retrocopies
retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Nomascus leucogenys ENSNLEG0000000833624 retrocopies
retro_nleu_1064, retro_nleu_1206, retro_nleu_1217, retro_nleu_1366, retro_nleu_1463, retro_nleu_1496, retro_nleu_165, retro_nleu_1694, retro_nleu_1748, retro_nleu_1969, retro_nleu_2120, retro_nleu_2452, retro_nleu_2678, retro_nleu_2791, retro_nleu_2833, retro_nleu_2834, retro_nleu_2950, retro_nleu_2955, retro_nleu_3021, retro_nleu_3047, retro_nleu_3052, retro_nleu_579, retro_nleu_850, retro_nleu_882,
Oryctolagus cuniculus ENSOCUG000000113732 retrocopies
retro_ocun_250, retro_ocun_874,
Otolemur garnettii ENSOGAG000000013655 retrocopies
retro_ogar_2166, retro_ogar_2314, retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Ochotona princeps ENSOPRG000000026932 retrocopies
retro_opri_297, retro_opri_800,
Procavia capensis ENSPCAG000000127951 retrocopy
retro_pcap_309,
Pongo abelii ENSPPYG000000165162 retrocopies
retro_pabe_2319, retro_pabe_97,
Pan troglodytes ENSPTRG0000001806326 retrocopies
retro_ptro_1021, retro_ptro_1090, retro_ptro_1092, retro_ptro_1126, retro_ptro_1160, retro_ptro_1287, retro_ptro_1335, retro_ptro_1391, retro_ptro_1497, retro_ptro_1502, retro_ptro_1503, retro_ptro_1788, retro_ptro_1918, retro_ptro_199, retro_ptro_2192, retro_ptro_2330, retro_ptro_2342, retro_ptro_238, retro_ptro_2519, retro_ptro_2793, retro_ptro_2797, retro_ptro_2919, retro_ptro_3051, retro_ptro_3078, retro_ptro_347, retro_ptro_603,
Rattus norvegicus ENSRNOG000000004904 retrocopies
retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii ENSSHAG00000000731 3 retrocopies
retro_shar_243, retro_shar_334 , retro_shar_724,
Ictidomys tridecemlineatus ENSSTOG000000134865 retrocopies
retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963,
Tupaia belangeri ENSTBEG0000000149216 retrocopies
retro_tbel_1302, retro_tbel_175, retro_tbel_1775, retro_tbel_2039, retro_tbel_2061, retro_tbel_2062, retro_tbel_2766, retro_tbel_2814, retro_tbel_314, retro_tbel_3359, retro_tbel_483, retro_tbel_522, retro_tbel_667, retro_tbel_980, retro_tbel_981, retro_tbel_986,
Tursiops truncatus ENSTTRG000000150642 retrocopies
retro_ttru_1089, retro_ttru_1211,


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