RetrogeneDB ID:

retro_shar_659

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL856941.1:362365..362848(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL18
Ensembl ID:ENSSHAG00000006564
Aliases:None
Description:ribosomal protein L18 [Source:HGNC Symbol;Acc:10310]


Retrocopy-Parental alignment summary:






>retro_shar_659
CTGTGGCTGCTAGTGAAGATGTACGAGTGTCTGGACCTCAGAACCAATCCAACTTTCAACAAAATTGTGCTGAACAGATT
ATTTATGAGCCAGATCAATCCCCTACCCCACACCCCATCCCTATCCCTGTCCCAAATGATCAGGAAAATGAAGTTGGCAG
GGAAAATAAGGATGGTTGCTGGGATGATGACAGATGATGTGAGGATCCAGGATGTCCCCAAGCTGAAGGTGTGCTCCTTT
TATATTACTAGTAATGCCCAGAAATGCATCCTCAAGGCTGGTGAGAAGACCCTCACCTTTAACCAGCTAGCCATGAGCTC
ACCCAAAGGCTAGGGCACTGTCCTGCTGTCTGGTCCCCAGGAGTATAGGCATTTTGGGAAGGCACTTGGCATTCCCCACA
GTTACCTTAAATGGTATGTCTGATCCAATGGCTGAAAATTTGGGTGTGCCAAGGGCTGCTGTGCCAGCCACAGCTACAAA
AAC

ORF - retro_shar_659 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.53 %
Parental protein coverage: 87.37 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLRLLVKLYRFLARRTNSTFNKVVLKRLFMSRTN----RPPLSLSRMIRKMKLPGRENKTAVVVGTVTDDV
L.LLVK.Y..L..RTN.TFNK.VL.RLFMS..N.....P.LSLS.MIRKMKL.G...K...V.G..TDDV
RetrocopyLWLLVKMYECLDLRTNPTFNKIVLNRLFMSQINPLPHTPSLSLSQMIRKMKLAG---KIRMVAGMMTDDV
ParentalRIQDVPKLKEQVCALRVTSNARSRILKAGGKILTFDQLAMSSPKGRGTVLLSGPRKGREVYRHFGKAPGT
RIQDVPKLK..VC....TSNA...ILKAG.K.LTF.QLAMSSPKG.GTVLLSGP......YRHFGKA.G.
RetrocopyRIQDVPKLK--VCSFYITSNAQKCILKAGEKTLTFNQLAMSSPKG*GTVLLSGPQE----YRHFGKALGI
ParentalPHSHTKPYVRSKGRKFERARGRRASRGYKN
PHS..K.YV.S.G.KF..A.G..AS..YKN
RetrocopyPHSYLKWYV*SNG*KFGCAKGCCASHSYKN

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_659 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 195 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000148723 retrocopies
retro_amel_1718, retro_amel_640, retro_amel_740,
Bos taurus ENSBTAG000000153881 retrocopy
retro_btau_845,
Canis familiaris ENSCAFG000000039677 retrocopies
retro_cfam_1285, retro_cfam_1383, retro_cfam_1507, retro_cfam_1853, retro_cfam_2044, retro_cfam_2199, retro_cfam_304,
Choloepus hoffmanni ENSCHOG000000091406 retrocopies
retro_chof_1408, retro_chof_1668, retro_chof_1697, retro_chof_2025, retro_chof_427, retro_chof_436,
Callithrix jacchus ENSCJAG000000003774 retrocopies
retro_cjac_1659, retro_cjac_2114, retro_cjac_2296, retro_cjac_529,
Cavia porcellus ENSCPOG000000263344 retrocopies
retro_cpor_1062, retro_cpor_1322, retro_cpor_703, retro_cpor_733,
Equus caballus ENSECAG000000219273 retrocopies
retro_ecab_478, retro_ecab_530, retro_ecab_880,
Erinaceus europaeus ENSEEUG000000158725 retrocopies
retro_eeur_176, retro_eeur_299, retro_eeur_381, retro_eeur_419, retro_eeur_437,
Echinops telfairi ENSETEG000000131576 retrocopies
retro_etel_1059, retro_etel_1211, retro_etel_1342, retro_etel_1373, retro_etel_1391, retro_etel_1715,
Felis catus ENSFCAG000000086524 retrocopies
retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Homo sapiens ENSG0000006317711 retrocopies
retro_hsap_1073, retro_hsap_1202, retro_hsap_1331, retro_hsap_1617, retro_hsap_1706, retro_hsap_3235, retro_hsap_3794, retro_hsap_3895, retro_hsap_4001, retro_hsap_4111, retro_hsap_772,
Gorilla gorilla ENSGGOG000000248787 retrocopies
retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Loxodonta africana ENSLAFG000000312671 retrocopy
retro_lafr_879,
Macropus eugenii ENSMEUG000000006401 retrocopy
retro_meug_1568,
Myotis lucifugus ENSMLUG0000000928612 retrocopies
retro_mluc_1440, retro_mluc_1442, retro_mluc_1462, retro_mluc_1736, retro_mluc_1791, retro_mluc_1912, retro_mluc_2023, retro_mluc_480, retro_mluc_729, retro_mluc_786, retro_mluc_886, retro_mluc_904,
Macaca mulatta ENSMMUG000000221583 retrocopies
retro_mmul_32, retro_mmul_55, retro_mmul_92,
Monodelphis domestica ENSMODG000000140991 retrocopy
retro_mdom_906,
Mustela putorius furoENSMPUG000000038914 retrocopies
retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Mus musculus ENSMUSG0000005907011 retrocopies
retro_mmus_1655, retro_mmus_2025, retro_mmus_2091, retro_mmus_2303, retro_mmus_2462, retro_mmus_2622, retro_mmus_2790, retro_mmus_3424, retro_mmus_3621, retro_mmus_726, retro_mmus_740,
Nomascus leucogenys ENSNLEG0000000453711 retrocopies
retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii ENSOGAG0000000356216 retrocopies
retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus ENSONIG000000065391 retrocopy
retro_onil_43,
Pongo abelii ENSPPYG000000102066 retrocopies
retro_pabe_1003, retro_pabe_1337, retro_pabe_1402, retro_pabe_2681, retro_pabe_3100, retro_pabe_3176,
Pan troglodytes ENSPTRG0000001124510 retrocopies
retro_ptro_1084, retro_ptro_1155, retro_ptro_2187, retro_ptro_2574, retro_ptro_2649, retro_ptro_2790, retro_ptro_540, retro_ptro_730, retro_ptro_822, retro_ptro_908,
Pteropus vampyrus ENSPVAG0000000952410 retrocopies
retro_pvam_101, retro_pvam_1034, retro_pvam_1244, retro_pvam_1376, retro_pvam_1444, retro_pvam_427, retro_pvam_785, retro_pvam_883, retro_pvam_969, retro_pvam_990,
Rattus norvegicus ENSRNOG0000002103514 retrocopies
retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii ENSSHAG00000006564 2 retrocopies
retro_shar_571, retro_shar_659 ,
Sus scrofa ENSSSCG000000259285 retrocopies
retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus ENSSTOG000000122585 retrocopies
retro_itri_261, retro_itri_323, retro_itri_828, retro_itri_853, retro_itri_957,
Tupaia belangeri ENSTBEG0000000159418 retrocopies
retro_tbel_1006, retro_tbel_126, retro_tbel_1591, retro_tbel_1599, retro_tbel_1600, retro_tbel_1719, retro_tbel_2618, retro_tbel_2628, retro_tbel_277, retro_tbel_2984, retro_tbel_3527, retro_tbel_3529, retro_tbel_3608, retro_tbel_3609, retro_tbel_4409, retro_tbel_4473, retro_tbel_4590, retro_tbel_737,
Tursiops truncatus ENSTTRG000000081873 retrocopies
retro_ttru_1127, retro_ttru_1770, retro_ttru_42,




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