RetrogeneDB ID:

retro_shar_216

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL834689.1:759785..760274(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7L1
Ensembl ID:ENSSHAG00000011219
Aliases:None
Description:ribosomal protein L7-like 1 [Source:HGNC Symbol;Acc:21370]


Retrocopy-Parental alignment summary:






>retro_shar_216
ATTCCCTTGGATCCATAGAAATTCCTGAAGAAGAGGAAAGCTTACTGAGCCCTCAAAATCTCGTAGGCTAAACTGGCACT
TTTGGAAAAGAGGAAGCATAAGTAAGAAAGTCAGCTCAAATTCAGGCAGCTGGAATCATTTCTCCATAAATCCCATTGGA
TAATCCATGATGTAGCCCATGTCAGGTCCCTGGATTTGCAGTCTGGGTGTTATGTGTGGAGGGATGCCCATCATCTGAAC
TTTCTGGTCCATATGAAGAGAATTAATGGAGTCAGTAACCAGGTTACAAAGATAATAGAGGCACATCATCTGAAGAAAAT
TTATAGTTCCATCTTTGTCAAAATTACCCCAACTTTCTCAAAGAAAGTGATAATTATAGAGTCTTATATCTTATATGACT
CAGGGATACCTAACCTGAAATTTATGTGTAATCTCAGTCTAAAATAAAGACAAGCAAGGATAAATAATAAGAAAGTCTCT
TTAATGGAT

ORF - retro_shar_216 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.96 %
Parental protein coverage: 65.98 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIPLVPENLLKKRKAYQALKATQAKQALLEKRKQKKGTQLKFRRLESFVHESHRVSRDVARLKRLVSKPGC
IPL.P...LKKRKAY.ALK...AK.ALLEKRK.K...QLKFR.LESF.H.SH....DVA....L....GC
RetrocopyIPLDP*KFLKKRKAY*ALKIS*AKLALLEKRKHK*ESQLKFRQLESFLHKSHWIIHDVAHVRSLDLQSGC
ParentalYVLKDAHRLAFVVRMEKINGVSNQVTKTIEELRLKKIYSGVFVKITPASLKKLRIIEPYVAW--GYPNLK
YV..DAH.L.F.V.M..INGVSNQVTK.IE...LKKIYS..FVKITP...KK..IIE.Y.....G.PNLK
RetrocopyYVWRDAHHLNFLVHMKRINGVSNQVTKIIEAHHLKKIYSSIFVKITPTFSKKVIIIESYILYDSGIPNLK
ParentalSVRELILKRGQARINNKKVSLTD
....L.LK..QARINNKKVSL.D
RetrocopyFMCNLSLK*RQARINNKKVSLMD

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_216 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 175 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000127912 retrocopies
retro_amel_1260, retro_amel_243,
Bos taurus ENSBTAG000000184782 retrocopies
retro_btau_588, retro_btau_816,
Canis familiaris ENSCAFG000000017284 retrocopies
retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni ENSCHOG000000003064 retrocopies
retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus ENSCPOG000000211892 retrocopies
retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus ENSDNOG000000134851 retrocopy
retro_dnov_689,
Equus caballus ENSECAG000000031131 retrocopy
retro_ecab_998,
Erinaceus europaeus ENSEEUG000000104311 retrocopy
retro_eeur_90,
Echinops telfairi ENSETEG000000024193 retrocopies
retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus ENSFCAG000000097071 retrocopy
retro_fcat_143,
Homo sapiens ENSG0000014622322 retrocopies
retro_hsap_1285, retro_hsap_1291, retro_hsap_1602, retro_hsap_1623, retro_hsap_1661, retro_hsap_1836, retro_hsap_2201, retro_hsap_2389, retro_hsap_2735, retro_hsap_2845, retro_hsap_3053, retro_hsap_3068, retro_hsap_3077, retro_hsap_3187, retro_hsap_3250, retro_hsap_3373, retro_hsap_3556, retro_hsap_3641, retro_hsap_3846, retro_hsap_3957, retro_hsap_4770, retro_hsap_4827,
Gorilla gorilla ENSGGOG0000000995815 retrocopies
retro_ggor_1009, retro_ggor_1013, retro_ggor_1253, retro_ggor_1261, retro_ggor_1904, retro_ggor_2099, retro_ggor_2108, retro_ggor_2113, retro_ggor_2162, retro_ggor_2282, retro_ggor_2457, retro_ggor_2524, retro_ggor_2591, retro_ggor_2659, retro_ggor_2973,
Macaca mulatta ENSMMUG000000213131 retrocopy
retro_mmul_11,
Monodelphis domestica ENSMODG000000190281 retrocopy
retro_mdom_1708,
Mustela putorius furoENSMPUG000000132961 retrocopy
retro_mputfur_1577,
Mus musculus ENSMUSG000000638884 retrocopies
retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Nomascus leucogenys ENSNLEG0000000464921 retrocopies
retro_nleu_1375, retro_nleu_1597, retro_nleu_1646, retro_nleu_1661, retro_nleu_2007, retro_nleu_2011, retro_nleu_2017, retro_nleu_2138, retro_nleu_2201, retro_nleu_2282, retro_nleu_2562, retro_nleu_2599, retro_nleu_2694, retro_nleu_2863, retro_nleu_2938, retro_nleu_332, retro_nleu_502, retro_nleu_536, retro_nleu_597, retro_nleu_711, retro_nleu_727,
Oryctolagus cuniculus ENSOCUG000000038446 retrocopies
retro_ocun_1393, retro_ocun_1604, retro_ocun_1818, retro_ocun_278, retro_ocun_509, retro_ocun_598,
Otolemur garnettii ENSOGAG000000126713 retrocopies
retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pongo abelii ENSPPYG0000001661921 retrocopies
retro_pabe_1064, retro_pabe_1069, retro_pabe_1315, retro_pabe_1341, retro_pabe_1370, retro_pabe_1379, retro_pabe_1457, retro_pabe_2078, retro_pabe_2154, retro_pabe_2354, retro_pabe_2527, retro_pabe_2543, retro_pabe_2598, retro_pabe_2609, retro_pabe_2644, retro_pabe_2988, retro_pabe_3053, retro_pabe_3259, retro_pabe_3410, retro_pabe_3714, retro_pabe_3753,
Pan troglodytes ENSPTRG0000001817523 retrocopies
retro_ptro_1074, retro_ptro_1088, retro_ptro_1127, retro_ptro_1162, retro_ptro_1671, retro_ptro_1849, retro_ptro_1927, retro_ptro_1987, retro_ptro_2069, retro_ptro_2076, retro_ptro_2198, retro_ptro_2257, retro_ptro_2293, retro_ptro_2416, retro_ptro_2466, retro_ptro_2622, retro_ptro_2686, retro_ptro_2916, retro_ptro_2933, retro_ptro_3212, retro_ptro_355, retro_ptro_878, retro_ptro_882,
Pteropus vampyrus ENSPVAG000000086963 retrocopies
retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus ENSRNOG000000162691 retrocopy
retro_rnor_2795,
Sorex araneus ENSSARG000000052862 retrocopies
retro_sara_100, retro_sara_211,
Sarcophilus harrisii ENSSHAG00000011219 1 retrocopy
retro_shar_216 ,
Sus scrofa ENSSSCG000000264723 retrocopies
retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus ENSSTOG000000098412 retrocopies
retro_itri_1233, retro_itri_417,
Tarsius syrichta ENSTSYG0000000484816 retrocopies
retro_tsyr_1312, retro_tsyr_1340, retro_tsyr_1380, retro_tsyr_1399, retro_tsyr_1729, retro_tsyr_1914, retro_tsyr_1933, retro_tsyr_2161, retro_tsyr_357, retro_tsyr_455, retro_tsyr_469, retro_tsyr_581, retro_tsyr_606, retro_tsyr_642, retro_tsyr_703, retro_tsyr_856,
Tursiops truncatus ENSTTRG000000069716 retrocopies
retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos ENSVPAG000000088942 retrocopies
retro_vpac_386, retro_vpac_584,


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