RetrogeneDB ID:

retro_shar_14

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL867785.1:39168..40959(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSHAG00000002700
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000005908
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_14
NCAGGCCCCGGGGGCGCCCCTCCGGCCGCCACGGCCGCCGCGGCCGAGGCCCAGAACCTCAGCGCGGCCTTGCGCGGCCA
GCTCACCGTCCGCGCTTCTGGGTTCGTGCAGTCCTCCTTGCGGGGCCCGGTTCGGCAGCCGCTGCCATCGCTGCCCCCAG
CCGCCGCCCGGGGAGACGGCTCCGGAGCAGGAGGCCCTGCTGGCCCCGAGGCACCTGTGGAACGTTCTCAAGAGCAGACA
GTGTCGTATGCAGGTTCAAAGTCAGCGCTCAGCATGGAAGGTTCAGGACCTGTTCTAAAAAGTGGAGAGACCGAGCTGTC
TCCAGAAGAATCATGGGAGCACAAAGAAGGACCGAGTGGAGCAGGACCGAGTGGAGCAGAACCGGGGGAAGGCTCTTTGG
GAGACAGAGGACCGCCAGAGGCGGGCGCGCCAGAAATGGTGGTGGAGAAGGAGGGAAAAATACCAAAACGCACATCTGTG
GTGGCACCAGCAGCTGCATCAAAAAAAGAACATGTAAACGTCGTATTCATTGGGCATGTGGATGCTGGCAAATCAACCAT
TGGAGGACAAATCATGTATTTGACGGGGATGGTTGACAAAAGAACACTTGAAAAATATCAACGAGAAGCTAAGGAAAAAA
ACAGAGAAACTTGGTACTTGTCCTGGGCCTTGGATACAAATCAGGAAGAACGAGACAAAGGTAAAACTGTGGAGGTGGGC
CGAGCCTACTTTGAGACAGAAAAAAAGCACTTCACCATCCTGGACGCCCCCGGGCACAAGAGTTTTGTCCCACACATGAT
TGGTGGCGCTTCTCAAGCCGATCTGGCCGTGCTGGTCATCTCTGCTCGGAAGGGAGAGTTTGAAACTGGATTTGAAAAAG
GAGGACAGACAAGGGAACATGCCATGTTGGCAAAAACAGCAGGTGTAAAGCACTTGATAGTGCTTGTGAACAAGATGGAT
GACCCAACAGTAAATTGGAGCAATAAGAGATATGAAGAATGCAAAGAAAAGTTGCTGCCATTTTTGAAAAAAGTTGGCTT
CAGTCCCAAAAAGGATATACACTTCATGCCCTGCTCAGGGCTGACAGGTGCAAACCTTAAAGAGCCGTCAGATTGCTGTC
CTTGGTATGAGGGGTTACCATTTGTTCAATATCTGGATGATTTGCCAAACTTCAACAGATCACTTGATGGACCAGTTAGG
CTGCCAATCGTGGATAAATACAAGGACATGGGCACTGTGGTCCTGGGAAAGTTGGAATCGGGCTCTATCTGTAAAGGACA
GCAGTTTGTGATGATGCCAAACAAGCACAATGTGGAAGTTCTTGGAATCCTTTCTGATGATGTAGAAACGGATTCTGCAG
CCCCAGGGGAAAACCTCAAGATTAGACTGAAGGGAATTGAAGAAGAAGAAATACTTCCAGGATTCATACTTTGTGAACCT
AAAAATCTCTGTCATTTTGGACGCACGTTTGATGCTCAGATAGTGATTATTGAGCACAAATCTATCATCTGCCCAGGTTA
TAATGCGGTGCTGCACATTCATACCTGTATCGAAGAAGTAGAGATAACAGCCTTAATCTGCTTGGTAGACAAAAAAACAG
GAGAAAAAAGTAAGACACGACCACGTTTTGTCAAACAAGATCAAGTATGCATTGCCCGTTTAAGAACAGCCGGAACCATC
TGCCTTGAGACCTTCAAAGATTTCCCTCAGATGGGTCGTTTTACCTTAAGAGATGAGGGGAAGACCATTGCAATTGGAAA
AGTTCTGAAACTGGTTCCAGAGAAGGACTAA

ORF - retro_shar_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.83 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPVEPSQEEQSVLYEGSNSAVSMEVSEPVVENGETEMSPEESWEHKEEPSEAESGGGSLGDGGPPEESVPE
PVE.SQE.Q.V.Y.GS.SA.SME.S.PV...GETE.SPEESWEHKE.PS.A...G...G.G.......PE
RetrocopyPVERSQE-QTVSYAGSKSALSMEGSGPVLKSGETELSPEESWEHKEGPSGAGPSGAEPGEGSLGDRGPPE
ParentalM----MMEEEE-EIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREA
.....M..E.E..IPK..SVVAP..A.KKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKY.REA
RetrocopyAGAPEMVVEKEGKIPKRTSVVAPAAASKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYQREA
ParentalKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVI
KEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVP.MIGGASQADLAVLVI
RetrocopyKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPHMIGGASQADLAVLVI
ParentalSARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPK
SARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVL.NKMDDPTVNWSN.RYEECKEKL.PFLKKVGF.PK
RetrocopySARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLVNKMDDPTVNWSNKRYEECKEKLLPFLKKVGFSPK
ParentalKDIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVLGKLES
KDIHFMPCSGLTGANLKE.SD.CPWY.GLPF..YLD.LPNFNRS.DGP.RLPIVDKYKDMGTVVLGKLES
RetrocopyKDIHFMPCSGLTGANLKEPSDCCPWYEGLPFVQYLDDLPNFNRSLDGPVRLPIVDKYKDMGTVVLGKLES
ParentalGSICKGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTF
GSICKGQQ.VMMPNKHNVEVLGILSDDVETDS.APGENLKIRLKGIEEEEILPGFILC.P.NLCH.GRTF
RetrocopyGSICKGQQFVMMPNKHNVEVLGILSDDVETDSAAPGENLKIRLKGIEEEEILPGFILCEPKNLCHFGRTF
ParentalDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTI
DAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKK.GEKSKTRPRFVKQDQVCIARLRTAGTI
RetrocopyDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKTGEKSKTRPRFVKQDQVCIARLRTAGTI
ParentalCLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
CLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyCLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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_14 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 25 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG000000188561 retrocopy
retro_cfam_2072,
Callithrix jacchus ENSCJAG000000181911 retrocopy
retro_cjac_618,
Cavia porcellus ENSCPOG000000093811 retrocopy
retro_cpor_73,
Equus caballus ENSECAG000000211951 retrocopy
retro_ecab_739,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG000000047281 retrocopy
retro_mdom_1420,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000622031 retrocopy
retro_mmus_238,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG00000005908 1 retrocopy
retro_shar_14 ,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


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