RetrogeneDB ID:

retro_shar_525

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL849806.1:181126..181603(+)
Located in intron of:ENSSHAG00000004749
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000015213
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_525
GACATAAAGATAAAGTTTTTGAAAAAAATAAATCTTTTCTCCATTCCTATCAGGCAGTCTGAGATAATAAACTTCTTCCT
AGGATCTTTGTTGAAATATGAAGTTCTGAAGATCTTACTTATGCAGAAACAAACTAGAGCTAGACAATAAACCTGGTTCA
AGGCTTTTTTGGTCGTTGCCAACTACAAAGGCCACATTGACCAGGGTTTCAAGTGCTCCAAGGAAGCAGGCACGGCTATT
CACGGTACCATCATTTTGGTCAAATTTTCCCTCATTCCTGTGAGATGCGGCTACTGGGAGAACAAGACTGGCAAGCCCCA
CATAGTGCCGTGCAAGGTCACTGGGCATTGTGGATCAGTTTTCATCCCTGCCCCTAAAAGTATTGGCATTGTCTCATCTC
CTGTGCCTAAGAAACTTCTGATGATGGATGGAATCGATGACTACTACTCTTCTGCAAGAGGCTGTACTGCCGCTCTG

ORF - retro_shar_525 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.9 %
Parental protein coverage: 55.29 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDMKIKSLEEIYLFSLPIKESEIIDFFLGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGV
D.KIK.L..I.LFS.PI..SEII.FFLGS.LK.EVLKI...QKQTRA.Q.T.FKAF.....Y.GH...G.
RetrocopyDIKIKFLKKINLFSIPIRQSEIINFFLGSLLKYEVLKILLMQKQTRARQ*TWFKAFLVVANYKGHIDQGF
ParentalKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPK
KCSKE..TAI.G.IIL.K.S..PVR.GYW.NK.GKPH.VPCKVTG.CGSV....IPAP...GIVS.PVPK
RetrocopyKCSKEAGTAIHGTIILVKFSLIPVRCGYWENKTGKPHIVPCKVTGHCGSV---FIPAPKSIGIVSSPVPK
ParentalKLLMMAGIDDCYTSARGCTATL
KLLMM.GIDD.Y.SARGCTA.L
RetrocopyKLLMMDGIDDYYSSARGCTAAL

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_525 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 31 parental genes, and 360 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
retro_acar_57,
Ailuropoda melanoleuca ENSAMEG000000073661 retrocopy
retro_amel_305,
Bos taurus ENSBTAG000000095357 retrocopies
retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris ENSCAFG0000001947219 retrocopies
retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Choloepus hoffmanni ENSCHOG000000123609 retrocopies
retro_chof_1056, retro_chof_2398, retro_chof_2545, retro_chof_2607, retro_chof_368, retro_chof_378, retro_chof_535, retro_chof_919, retro_chof_989,
Callithrix jacchus ENSCJAG0000001526715 retrocopies
retro_cjac_1482, retro_cjac_1585, retro_cjac_1609, retro_cjac_1712, retro_cjac_1964, retro_cjac_2201, retro_cjac_2255, retro_cjac_2284, retro_cjac_2361, retro_cjac_2493, retro_cjac_2620, retro_cjac_274, retro_cjac_317, retro_cjac_3741, retro_cjac_4194,
Cavia porcellus ENSCPOG0000001165111 retrocopies
retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Dipodomys ordii ENSDORG0000000737518 retrocopies
retro_dord_163, retro_dord_206, retro_dord_215, retro_dord_284, retro_dord_392, retro_dord_445, retro_dord_465, retro_dord_499, retro_dord_500, retro_dord_505, retro_dord_568, retro_dord_571, retro_dord_572, retro_dord_683, retro_dord_703, retro_dord_711, retro_dord_723, retro_dord_89,
Equus caballus ENSECAG000000090657 retrocopies
retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Felis catus ENSFCAG000000291916 retrocopies
retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Homo sapiens ENSG0000014098847 retrocopies
retro_hsap_1060, retro_hsap_136, retro_hsap_140, retro_hsap_141, retro_hsap_1443, retro_hsap_1444, retro_hsap_1457, retro_hsap_1463, retro_hsap_148, retro_hsap_1648, retro_hsap_1688, retro_hsap_1722, retro_hsap_1812, retro_hsap_1830, retro_hsap_1831, retro_hsap_1838, retro_hsap_1845, retro_hsap_1897, retro_hsap_1953, retro_hsap_1965, retro_hsap_1971, retro_hsap_2124, retro_hsap_2198, retro_hsap_2424, retro_hsap_244, retro_hsap_2483, retro_hsap_2486, retro_hsap_250, retro_hsap_282, retro_hsap_2871, retro_hsap_3035, retro_hsap_3097, retro_hsap_3106, retro_hsap_3182, retro_hsap_3211, retro_hsap_3369, retro_hsap_3464, retro_hsap_3584, retro_hsap_3779, retro_hsap_385, retro_hsap_4094, retro_hsap_4290, retro_hsap_435, retro_hsap_4811, retro_hsap_754, retro_hsap_761, retro_hsap_970,
Gorilla gorilla ENSGGOG000000093715 retrocopies
retro_ggor_129, retro_ggor_1391, retro_ggor_1428, retro_ggor_168, retro_ggor_390,
Loxodonta africana ENSLAFG0000000469611 retrocopies
retro_lafr_1072, retro_lafr_1092, retro_lafr_1103, retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376, retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii ENSMEUG000000045082 retrocopies
retro_meug_156, retro_meug_2103,
Microcebus murinus ENSMICG0000001276528 retrocopies
retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Myotis lucifugus ENSMLUG000000116601 retrocopy
retro_mluc_76,
Monodelphis domestica ENSMODG000000160771 retrocopy
retro_mdom_536,
Mustela putorius furoENSMPUG0000001554711 retrocopies
retro_mputfur_1100, retro_mputfur_1209, retro_mputfur_1212, retro_mputfur_1214, retro_mputfur_1391, retro_mputfur_1497, retro_mputfur_1566, retro_mputfur_369, retro_mputfur_540, retro_mputfur_624, retro_mputfur_931,
Mus musculus ENSMUSG000000445331 retrocopy
retro_mmus_148,
Nomascus leucogenys ENSNLEG000000088771 retrocopy
retro_nleu_2895,
Otolemur garnettii ENSOGAG0000001009819 retrocopies
retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835, retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842, retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Procavia capensis ENSPCAG000000020902 retrocopies
retro_pcap_251, retro_pcap_433,
Pteropus vampyrus ENSPVAG000000167048 retrocopies
retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus ENSRNOG0000001417912 retrocopies
retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii ENSSHAG00000015213 5 retrocopies
retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525 , retro_shar_783,
Sus scrofa ENSSSCG000000228598 retrocopies
retro_sscr_280, retro_sscr_293, retro_sscr_412, retro_sscr_486, retro_sscr_729, retro_sscr_803, retro_sscr_950, retro_sscr_951,
Ictidomys tridecemlineatus ENSSTOG000000129444 retrocopies
retro_itri_1239, retro_itri_1666, retro_itri_1680, retro_itri_221,
Tupaia belangeri ENSTBEG0000000672630 retrocopies
retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129, retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,
Tarsius syrichta ENSTSYG0000001346652 retrocopies
retro_tsyr_1069, retro_tsyr_1078, retro_tsyr_1147, retro_tsyr_1301, retro_tsyr_131, retro_tsyr_1317, retro_tsyr_1466, retro_tsyr_1478, retro_tsyr_1498, retro_tsyr_1505, retro_tsyr_1509, retro_tsyr_1536, retro_tsyr_1564, retro_tsyr_1568, retro_tsyr_1588, retro_tsyr_1614, retro_tsyr_1636, retro_tsyr_1658, retro_tsyr_169, retro_tsyr_1789, retro_tsyr_1804, retro_tsyr_1827, retro_tsyr_186, retro_tsyr_1929, retro_tsyr_1935, retro_tsyr_2016, retro_tsyr_2175, retro_tsyr_290, retro_tsyr_349, retro_tsyr_415, retro_tsyr_417, retro_tsyr_463, retro_tsyr_472, retro_tsyr_525, retro_tsyr_527, retro_tsyr_545, retro_tsyr_568, retro_tsyr_604, retro_tsyr_605, retro_tsyr_609, retro_tsyr_61, retro_tsyr_622, retro_tsyr_638, retro_tsyr_650, retro_tsyr_672, retro_tsyr_689, retro_tsyr_691, retro_tsyr_699, retro_tsyr_768, retro_tsyr_773, retro_tsyr_922, retro_tsyr_980,
Tursiops truncatus ENSTTRG0000001139312 retrocopies
retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos ENSVPAG000000068676 retrocopies
retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,


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