RetrogeneDB ID:

retro_shar_458

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL849560.1:577892..578161(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000006890
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_458
AACACTATCTCCATTGCCATTTGAAAGGACAATGAGATCCAGGTGATTAGTGGACACTATGAAAGTCAGAAAATTAACAA
GTTAATACAGGTCTACAGAAAAAATACATCATGTACATTGAGTGTGTGCAATGTGAACAAGCTAATGGCATAACTGCCCA
CATTTGCATTCATCCTGCCAAGGGAGTGATCTCCAAGTCAAAAGACGGCAAAGATCACAAAAGAATTTTTAAGTGTAAAG
TTAAATGCTAATATGTTGGAAAGGAGAAG

ORF - retro_shar_458 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.95 %
Parental protein coverage: 62.07 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalNVRSMPIRKDDEVQVVRGHYKGQQIGKVVQVYRK-KYVIYIERVQREKANGTTVHVGIHPSKVVITRLKL
N..S..I.KD.E.QV..GHY..Q.I.K..QVYRK.KY..YIE.VQ.E.ANG.T.H..IHP.K.VI...K.
RetrocopyNTISIAI*KDNEIQVISGHYESQKINKLIQVYRK<KYIMYIECVQCEQANGITAHICIHPAKGVISKSKD
ParentalDKDRKKILERKAKSRQVGKEK
.KD.K.I...K.K...VGKEK
RetrocopyGKDHKRIFKCKVKC*YVGKEK

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_458 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 28 parental genes, and 277 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024537 retrocopies
retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus ENSBTAG000000123442 retrocopies
retro_btau_1090, retro_btau_230,
Choloepus hoffmanni ENSCHOG0000000470310 retrocopies
retro_chof_149, retro_chof_1893, retro_chof_2147, retro_chof_2276, retro_chof_2333, retro_chof_2383, retro_chof_244, retro_chof_312, retro_chof_816, retro_chof_942,
Callithrix jacchus ENSCJAG000000143728 retrocopies
retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Cavia porcellus ENSCPOG0000000131510 retrocopies
retro_cpor_1009, retro_cpor_1161, retro_cpor_1346, retro_cpor_1421, retro_cpor_1503, retro_cpor_1526, retro_cpor_167, retro_cpor_522, retro_cpor_585, retro_cpor_858,
Dasypus novemcinctus ENSDNOG000000024703 retrocopies
retro_dnov_2054, retro_dnov_2174, retro_dnov_378,
Equus caballus ENSECAG000000157574 retrocopies
retro_ecab_429, retro_ecab_473, retro_ecab_515, retro_ecab_609,
Felis catus ENSFCAG0000001125913 retrocopies
retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens ENSG0000016197027 retrocopies
retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla ENSGGOG000000239444 retrocopies
retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Macropus eugenii ENSMEUG000000098917 retrocopies
retro_meug_1239, retro_meug_1538, retro_meug_1607, retro_meug_1827, retro_meug_262, retro_meug_322, retro_meug_534,
Myotis lucifugus ENSMLUG000000021761 retrocopy
retro_mluc_232,
Macaca mulatta ENSMMUG0000000344822 retrocopies
retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica ENSMODG000000062012 retrocopies
retro_mdom_36, retro_mdom_64,
Mustela putorius furoENSMPUG0000000798812 retrocopies
retro_mputfur_1003, retro_mputfur_1146, retro_mputfur_1385, retro_mputfur_1428, retro_mputfur_1595, retro_mputfur_251, retro_mputfur_365, retro_mputfur_395, retro_mputfur_488, retro_mputfur_522, retro_mputfur_643, retro_mputfur_685,
Mus musculus ENSMUSG0000006093821 retrocopies
retro_mmus_1325, retro_mmus_1444, retro_mmus_1506, retro_mmus_1642, retro_mmus_1866, retro_mmus_1978, retro_mmus_2011, retro_mmus_2218, retro_mmus_2435, retro_mmus_2540, retro_mmus_2673, retro_mmus_3078, retro_mmus_3174, retro_mmus_320, retro_mmus_3270, retro_mmus_3291, retro_mmus_3361, retro_mmus_384, retro_mmus_556, retro_mmus_900, retro_mmus_939,
Nomascus leucogenys ENSNLEG000000099811 retrocopy
retro_nleu_76,
Oryctolagus cuniculus ENSOCUG0000000653811 retrocopies
retro_ocun_1125, retro_ocun_1290, retro_ocun_1442, retro_ocun_1484, retro_ocun_1515, retro_ocun_1621, retro_ocun_1917, retro_ocun_529, retro_ocun_542, retro_ocun_589, retro_ocun_803,
Otolemur garnettii ENSOGAG000000170703 retrocopies
retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes ENSPTRG000000087423 retrocopies
retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus ENSRNOG000000042143 retrocopies
retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sorex araneus ENSSARG0000000579813 retrocopies
retro_sara_172, retro_sara_208, retro_sara_228, retro_sara_273, retro_sara_319, retro_sara_334, retro_sara_393, retro_sara_527, retro_sara_578, retro_sara_627, retro_sara_641, retro_sara_656, retro_sara_740,
Sarcophilus harrisii ENSSHAG00000006890 1 retrocopy
retro_shar_458 ,
Sus scrofa ENSSSCG000000288509 retrocopies
retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus ENSSTOG000000219236 retrocopies
retro_itri_1113, retro_itri_1145, retro_itri_1206, retro_itri_1262, retro_itri_1670, retro_itri_811,
Tupaia belangeri ENSTBEG0000000774953 retrocopies
retro_tbel_1053, retro_tbel_1088, retro_tbel_1103, retro_tbel_1140, retro_tbel_1366, retro_tbel_1389, retro_tbel_1390, retro_tbel_1391, retro_tbel_1433, retro_tbel_1497, retro_tbel_1512, retro_tbel_1767, retro_tbel_1793, retro_tbel_1928, retro_tbel_1930, retro_tbel_2005, retro_tbel_2033, retro_tbel_2053, retro_tbel_2057, retro_tbel_2099, retro_tbel_2105, retro_tbel_2332, retro_tbel_2416, retro_tbel_2465, retro_tbel_2500, retro_tbel_268, retro_tbel_2727, retro_tbel_2778, retro_tbel_2806, retro_tbel_2884, retro_tbel_3020, retro_tbel_3187, retro_tbel_3300, retro_tbel_3332, retro_tbel_3704, retro_tbel_3711, retro_tbel_3790, retro_tbel_3964, retro_tbel_404, retro_tbel_4162, retro_tbel_4200, retro_tbel_4381, retro_tbel_4416, retro_tbel_446, retro_tbel_4480, retro_tbel_470, retro_tbel_474, retro_tbel_495, retro_tbel_573, retro_tbel_863, retro_tbel_906, retro_tbel_964, retro_tbel_99,
Tarsius syrichta ENSTSYG0000000148317 retrocopies
retro_tsyr_1273, retro_tsyr_1274, retro_tsyr_1499, retro_tsyr_153, retro_tsyr_1705, retro_tsyr_1858, retro_tsyr_1869, retro_tsyr_2152, retro_tsyr_262, retro_tsyr_327, retro_tsyr_346, retro_tsyr_600, retro_tsyr_636, retro_tsyr_684, retro_tsyr_808, retro_tsyr_865, retro_tsyr_905,
Vicugna pacos ENSVPAG000000002794 retrocopies
retro_vpac_214, retro_vpac_255, retro_vpac_26, retro_vpac_357,


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