RetrogeneDB ID:

retro_shar_127

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL849829.1:667430..669353(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSHAG00000010315
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000017568
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_127
ATGGCAGATAAACTCCCTTCAGAATTCGATGTGATTGTTATCGGAACTGGTTTGCCTGAGTCCATTGTTGCAGCTGCTTG
TTCAAGAAGTGGCCAAAGTGTTCTACATGTGGATTCAAGAAGTTATTATGGAGGAAACTGGGCTGGTTTCAATTTTTCAG
AACTATTATCTTGGATAAAAAAATATCAGGAAGAGAGTGATGTTGGAGTCGATTGGGCAGCATGTCAAGAGCTAATACTG
GAAACAGAAGAAGCCATTGTTCTTACAAAGAAAGATCAGACCATCCAACATGTAGAAGTCATTTGTTATGTCACTCAGGA
TTCAGATGATCACATTGAAAAAGTTGGTGCTTTGGAGAAGAATCCTGTCTCTGTGATGTCTCCTAGACCAAATGACCCTC
TAATCACAATGTACACAGCTTGCTCTGATACATCTGAATTGCCATTACCACACAGTGAGTCAGAGACTGCACTAGAAGGC
CCTGAAGTAGATGTGATGCTAGAGAAAGAATATCATGAAAATTATACAGAATTTAGCCAGTCAGCCTTGGAGCCGGAAAA
AGCTGAAAATGTACCAATCATAGAAGATGTTGCTGCTACACCCAAGAAGAAAAGAATTACTTACTCCCAAATTATTAAAG
AAGGCAGGAAATTTAATATTGATTTGACCTCTAAGCTTCTTTATTCTCGAGGATTGTTAATTGACCTTCTAATCAAATCA
AATGTTAGTCGTTATGCAGAGTTCAAAAATGTTACTAGAATTCTTGGATATCAAGAAGAGAATGTGCTACTGGTACCTTG
CTCCAGAGCAGATGTTTTTAATAGCAAAAAACTCACTATGGTAGAAAAAAGAATGCTGATGAAATTTTTGACATTTTGTT
TAGACTATGAACAGCACCCTGATGAATACAAAGCTTATGAGGAAAGTACCTTTTCAGAATACTTAAAAACTCAAAAACTG
ACACCCAACCTGAGGCACTTTGTTCTTCATTCCATGGCAATGATTTCAGAAACATCCAGCAGCACCTTAGATGGCCTCAG
AGAAACAAGGAACTTTCTTCAATGTCTTGGGCAATATGGCAATACTCCCTTTTTGTTCCCATTGTATGGTCAAGGAGAAA
TACCCCAGGGTTTCTGTAGAATGTGTGCAGTATTTGGTGGAACATATTGTCTTAACCATGAAGTACAGTGCCTTGTAGTA
GACAAAGAATCTGGAAAGTGCAAGGCAATCATAGATCGTACTGGTCAGAGAATAAATGCTAAGTATTTTATTGTTGAAGA
TAGTTGCCTTTCTGAGAAAACATGTTCAAATGTGACCTATAAGCAGATATCGAGGGCAGTCCTGATCACAGATCTATCTA
TACTGAAGGCAGATTCTGATCAGCACATTTCCATTTTGACAATGCCATCAATAGACCCAGGGTCTGCTCCTGTCCGCCTC
ATTGAGTTGTGCTCTTCAACAATGACATGCATGGAAGGAACATATCTTGTCCATTTGACTTGTGCATCCTCAAAAAAAAC
AGCAAGAGAAGATTTAGAATTGGTTGTACAAAAATTATTCACCCCATATACTGAAGTGGAGCTGGACAAAAGGGAACAAG
AAAAGCCAAATCTTCTGTGGGCCCTCTATTTCAACATGAGAGATTCTTCAGGCATTAATAGAGACTCCTATAGTGACTTA
CCTTCAAACATGTACATCTGCTCTGGACCAGACTGTTTTTTGGGAAGTGAGCATGCTGTTAAACAGGCTCAAACATTTTT
TCAGCACATCTTGCCAAATGAAGAGTTTTGCCCCCCTCCACCAAATCCTGAAGATATTATATTTGATGGAGATAGTGGGC
AACCAGAAATTCTTGCATCCAAGCCAGACACTGCTGAAGAAGTCACAGGCCAAAGAAACCCAGAAGAACATGCTCCTGAA
TAG

ORF - retro_shar_127 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.46 %
Parental protein coverage: 99.37 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADKLPSEFDVVVIGTGLPESIIAAACSRSGQSVLHVDSRSYYGGNWASFSFSGLLSWIKEYQEENN-GE
MADKLPSEFDV.VIGTGLPESI.AAACSRSGQSVLHVDSRSYYGGNWA.F.FS.LLSWIK.YQEE...G.
RetrocopyMADKLPSEFDVIVIGTGLPESIVAAACSRSGQSVLHVDSRSYYGGNWAGFNFSELLSWIKKYQEESDVGV
ParentalEWTAWQELILETEEGVALRKKDQTIQHVEVICYASQDSDEHVEEVGAVQKNPGSVTSASTNDPPDSMVTA
.W.A.QELILETEE...L.KKDQTIQHVEVICY..QDSD.H.E.VGA..KNP.SV.S...NDP...M.TA
RetrocopyDWAACQELILETEEAIVLTKKDQTIQHVEVICYVTQDSDDHIEKVGALEKNPVSVMSPRPNDPLITMYTA
ParentalCSDTSELTTPLSEPEAAREVPDVDVTLGNENHGGDTDCSQSPLEQEKAGNLPVGEDVVDAPKKNRITYSQ
CSDTSEL..P.SE.E.A.E.P.VDV.L..E.H...T..SQS.LE.EKA.N.P..EDV...PKK.RITYSQ
RetrocopyCSDTSELPLPHSESETALEGPEVDVMLEKEYHENYTEFSQSALEPEKAENVPIIEDVAATPKKKRITYSQ
ParentalIVKEGRRFNIDLTSKLLYSRGLLIDLLIKSNVSRYAEFKNVTRILGYQEGNVLQVPCSRADVFNSKKLTM
I.KEGR.FNIDLTSKLLYSRGLLIDLLIKSNVSRYAEFKNVTRILGYQE.NVL.VPCSRADVFNSKKLTM
RetrocopyIIKEGRKFNIDLTSKLLYSRGLLIDLLIKSNVSRYAEFKNVTRILGYQEENVLLVPCSRADVFNSKKLTM
ParentalVEKRMLMKFLTFCLDYEQQPDEYKAYEECTFSEYLKTQKLTPNLQHFVLHSIAMTSEESTSTLDGLRETQ
VEKRMLMKFLTFCLDYEQ.PDEYKAYEE.TFSEYLKTQKLTPNL.HFVLHS.AM.SE.S.STLDGLRET.
RetrocopyVEKRMLMKFLTFCLDYEQHPDEYKAYEESTFSEYLKTQKLTPNLRHFVLHSMAMISETSSSTLDGLRETR
ParentalNFLRCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGTYCLSHAVQCLVVDKESGKCKAIIDHFGQRISA
NFL.CLG.YGNTPFLFPLYGQGE.PQ.FCRMCAVFGGTYCL.H.VQCLVVDKESGKCKAIID..GQRI.A
RetrocopyNFLQCLGQYGNTPFLFPLYGQGEIPQGFCRMCAVFGGTYCLNHEVQCLVVDKESGKCKAIIDRTGQRINA
ParentalKYFIVEDSYLTEKTCSNVTYRQISRAVLITDQSVLKADSDQQISILTVPPVEPGSEAVRVVELCSSTMTC
KYFIVEDS.L.EKTCSNVTY.QISRAVLITD.S.LKADSDQ.ISILT.P...PGS..VR..ELCSSTMTC
RetrocopyKYFIVEDSCLSEKTCSNVTYKQISRAVLITDLSILKADSDQHISILTMPSIDPGSAPVRLIELCSSTMTC
ParentalMKGTYLVHLTCPSSKKTAREDLESVVQKLFTPYAEAELENEELKKPNLLWALYFNMRDSSDISRECYNDL
M.GTYLVHLTC.SSKKTAREDLE.VVQKLFTPY.E.EL...E..KPNLLWALYFNMRDSS.I.R..Y.DL
RetrocopyMEGTYLVHLTCASSKKTAREDLELVVQKLFTPYTEVELDKREQEKPNLLWALYFNMRDSSGINRDSYSDL
ParentalPSNVYVCCGPDGFLGNKNAVKQAEALFRLILPNEEFCPPPPNPEDIVFDGDGLQPELSSPKPEDAKEITD
PSN.Y.C.GPD.FLG...AVKQA...F..ILPNEEFCPPPPNPEDI.FDGD..QPE....KP..A.E.T.
RetrocopyPSNMYICSGPDCFLGSEHAVKQAQTFFQHILPNEEFCPPPPNPEDIIFDGDSGQPEILASKPDTAEEVTG
ParentalQGEVEE
Q...EE
RetrocopyQRNPEE

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_127 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 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000056501 retrocopy
retro_shar_43,
Sarcophilus harrisii ENSSHAG00000017568 1 retrocopy
retro_shar_127 ,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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