RetrogeneDB ID:

retro_shar_81

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL861690.1:529500..531339(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSHAG00000009314
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000016649
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_81
ATGGGGAGAAGATCTGCATCATGCACCAAGAATGGGAAGTTCATGAACTCCACTGACCAGGCTCGAAAGGAAGCTCGGAA
GAGGGAATTAAAAAAGAATAAGAAACAACGAATGATGGTAAGAGAAGCAATACTGAAGATGAAGGATCCCAAACAGATTA
TCTGGGACATGGAAAAACTGGATGAGATGGAGTTCAATCCCGTACAGCAGCCACAGCTAAATGGAAATGTGATCAAAAGG
AAACGCAAAAAACTTCAGGAAACTTTTCATAGCATTGTCCGACTGTATGAAAAGGAAAATCCAGATATCGCCAAAGAACT
TGGAAACTTAGAGGTGCAGTGTGAGCAGAAGAGGGCCCAGCTCAGTCAATACTTTGATGCTATAAAGAATGCTCAGCAAG
TTGAAGTGGAAAGCATCCCACTGCCTGCAATGCCTCATGTTCCTTCTAACATCTCAGTCCAAGGAATGCCATTGCCTGGT
GCACGGTCATCAACTGTTCTCAAAAATCTCTCTGCCTATCGACCTCCCACCAGGGCAATTTCTCTGCTTTCTTTGCCTGG
ACATGGCGTTCCTCCTTTACCTCCTGGCAGACTTCCTCCGGGCCCACCCCCTGGGCCACCACCTTTCCAAGTTCTGCAGA
TGTATGGCCGTAAAGTGGGCTTTGCTCTAGAGCTTGTTCCTCCTCAGCAGCAGGAGGATAGTTTTTATAGTCCAGAATTT
GCTCAAGGAGGTCATGATGACGATGCTTTCGGCACTATTGAAAAAGAAGATTGTTCTCAAGACGTGCATCAAAATAAGCA
CGATGACAGCAGTCGTGACAGGGACACTGACAAGTCAGATATCCTCTGGGAAGAAAAGTTCATGGCTGATGATGAAGAGA
GAGAGAACAGTGAAGAAAAAAACTCAGTTCTCAATGTAAGATTTGCTGGTGTTCCTGGACAATCAGAAAAGAAAAAGAAA
AACATGAAGAAATTAACACCTCTTCAAGCTGCCATGCTTAGAATCGCAGATCAGGAAATTCCTGAAGAGGGGCAAGAAGC
TTGGGTATTTTCAGAGGATGATGACCAGGAGGATTCTGAGGACTCCAGGGACACAAGACTGCCGCAGCACAAGGAAGCAT
CTCTTCTGGATGGGGCATTCTCATCTCCTGCTTCTCAGCAACAGCAACCACCTCCACAGTCTGTTCTTCCTGCCCAAAGA
CAGTTGCCTGCCATACCAGGACTCCACCCTGCTCCACCATTACTACCAGCTCTTGGGCTCCCTCCTGTTCCACCCCTGGG
AGCTACTCCCTTCTTAAAACCACTTGCAATGCCAGAGTTTAGAGGGCCTTCACCCAAGCTTTTACTTTCTGGCCCTTCTC
CTCAAGGGGGACCACCAAAGCTATGTCCCCCAGCACCTCTAGCCAGTCCTCCACCTCCTCCTGGGAGGACAAACCCACCT
TTTGTACCCCAACTTGCACCAGCTCCACCTGGGCTTTATCCATCAGCTCCCTTGGCCAGTCCACAGATTTTAAGTGCTCC
ACCCAATTTGATCCAGAGATCTAAAATGCATGATACCACTGCAGCTCCCATTGAGAAGAAAGTCACAGCTATCATCAGCG
CCAAGCCACAAATCACCAATCCCAAGGCAGAAATGATCAGATTTGTGCCCACTGCATTGAGGATTCAACGAGAAAACAAA
AGAGCTACTGCTGCTGTTCCCCAAGGGAAGTCGGAAAAGGATTTTACTATACCCCTTGCCAAAACCGTCCCTCAATCTGG
CCCCTCTGATCCTGTTTCAGTACAGACCAAGGACGATGTGTATGAGGCTTTCATGAAAGAGATGGAGGGGTTACTCTGA

ORF - retro_shar_81 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.65 %
Parental protein coverage: 78.69 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGRRSTSSTKSGKFMNPTDQARKEARKRELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQQ
MGRRS.S.TK.GKFMN.TDQARKEARKRELKKNKKQRMMVR.A.LKMKDPKQII.DMEKLDEMEFNPVQQ
RetrocopyMGRRSASCTKNGKFMNSTDQARKEARKRELKKNKKQRMMVREAILKMKDPKQIIWDMEKLDEMEFNPVQQ
ParentalPQLNEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIP
PQLN..V.K.KRKKL.ETF..I.RLYEKENPDI.KEL..LEV..EQKRAQLSQYFDA.KNAQ.VEVESIP
RetrocopyPQLNGNVIKRKRKKLQETFHSIVRLYEKENPDIAKELGNLEVQCEQKRAQLSQYFDAIKNAQQVEVESIP
ParentalLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAISILPLLGHGVPRLPPGRKPPGPPPGPPPPQ
LP.MPH.PSNI..Q..PLPGA.....LK..SAY.PPTRAIS.L.L.GHGVP.LPPGR.PPGPPPGPPP.Q
RetrocopyLPAMPHVPSNISVQGMPLPGARSSTVLKNLSAYRPPTRAISLLSLPGHGVPPLPPGRLPPGPPPGPPPFQ
ParentalVLQMYGRKVGFALELAPRRREEDILYSPELAHRGHDDDGSSTSEDEGYPEDMDQDKHDDSSDDSDTDRSD
VLQMYGRKVGFALEL.P....ED..YSPE.A..GHDDD...T.E.E....D..Q.KHDDSS.D.DTD.SD
RetrocopyVLQMYGRKVGFALELVPPQQQEDSFYSPEFAQGGHDDDAFGTIEKEDCSQDVHQNKHDDSSRDRDTDKSD
ParentalADSEGEEFMHRDDEERENNEDKKSGLSVRFADVPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVE
...E.E.FM..DDEEREN.E.K.S.L.VRFA.VPG.S.KKKKNMK.LTPLQA.MLR.A.QEIPEEG.E..
RetrocopyILWE-EKFM-ADDEERENSEEKNSVLNVRFAGVPGQSEKKKKNMKKLTPLQAAMLRIADQEIPEEGQEAW
ParentalEFSEDDDEEDSDDSESEDTTQQQHKEETLPDGASSSPVSQQQQPPPQSVPPTQIQAPPMPGPPPLGPPPA
.FSEDDD.EDS.D..S.DT...QHKE..L.DGA.SSP.SQQQQPPPQSV.P.Q.Q.P..PG..P..PP..
RetrocopyVFSEDDDQEDSED--SRDTRLPQHKEASLLDGAFSSPASQQQQPPPQSVLPAQRQLPAIPGLHP-APPLL
ParentalPPL-RPPGPPTGLPPGPPPGAPPFLRPPGMP-GLRGPLPRLLPPGPPPGRPPGPPPGPPPGLPPGPPPRG
P.L..PP.PP.G..P...P.A.P..R.P.....L.GP.P.....GPP...PP.P...PPP..PPG...R.
RetrocopyPALGLPPVPPLGATPFLKPLAMPEFRGPSPKLLLSGPSPQ---GGPPKLCPPAPLASPPP--PPG---RT
ParentalPPPRLP--PPAPPGIPPPRP
.PP..P...PAPPG..P..P
RetrocopyNPPFVPQLAPAPPGLYPSAP

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_81 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 22 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147591 retrocopy
retro_btau_20,
Canis familiaris ENSCAFG000000129262 retrocopies
retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus ENSCJAG000000216111 retrocopy
retro_cjac_1737,
Homo sapiens ENSG000000844632 retrocopies
retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla ENSGGOG000000044483 retrocopies
retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii ENSMEUG000000139711 retrocopy
retro_meug_1952,
Myotis lucifugus ENSMLUG000000152161 retrocopy
retro_mluc_1074,
Macaca mulatta ENSMMUG000000192991 retrocopy
retro_mmul_1329,
Monodelphis domestica ENSMODG000000179491 retrocopy
retro_mdom_143,
Mustela putorius furoENSMPUG000000116191 retrocopy
retro_mputfur_280,
Mus musculus ENSMUSG000000302161 retrocopy
retro_mmus_2740,
Nomascus leucogenys ENSNLEG000000039261 retrocopy
retro_nleu_2651,
Oryctolagus cuniculus ENSOCUG000000171771 retrocopy
retro_ocun_974,
Otolemur garnettii ENSOGAG000000105181 retrocopy
retro_ogar_207,
Ochotona princeps ENSOPRG000000150083 retrocopies
retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii ENSPPYG000000043233 retrocopies
retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes ENSPTRG000000047243 retrocopies
retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus ENSRNOG000000055053 retrocopies
retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus ENSRNOG000000495931 retrocopy
retro_rnor_740,
Sorex araneus ENSSARG000000070851 retrocopy
retro_sara_753,
Sarcophilus harrisii ENSSHAG00000016649 1 retrocopy
retro_shar_81 ,
Tupaia belangeri ENSTBEG000000033941 retrocopy
retro_tbel_2213,


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