RetrogeneDB ID:

retro_shar_24

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL867819.1:63247..65152(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSHAG00000003431
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSHAG00000011267
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_shar_24
ATGCACCCCAGCGCCCCCAGCTACCCCACGGCCTCGCTGTACGTGGGGGACCTGCACCCCGAGGTGAGCGAGGCGATGCT
GTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGCGTCTGCAGGGACATGATCACCAGGCGCTCCCTGGGCT
ACGCCTATGTCAACTTCCAGCAGCCGGCGGATGCCGAGAGAGCCCTGGAGACCATGAATTTCGATGTCATCAAGGGCAAG
CCGGTGCGCATCATGTGGTCCCAGAGGGACCCCTCCCTCCGCAAAAGCGGCGTGGGCAACATCTTCATCAAAAACCTGGA
CAAGTCCATCGACAACAAGGCTCTGTTCGATACCTTCTCCGCCTTCGGCAACATCCTGTCCTGCAAGGTGGTGTGCGACG
AGAACGGCTCCAAGGGCTACGGGTTCGTGCACTTCGAGACCCGCGAGGCGGCCGAGAGGGCCATCGACAAGATGAACGGC
ATGCTCCTGAACGACCGCAAGGTCTTCGTGGGCCGCTTTAAGTCCCGCAAAGAGAGGGAGGCCGAGCTGGGGGCCAGGGC
CAAAGAGTTCACCAACGTTTACATCAAGAACTTCGGGGAGGACATGGACGATCTGAGGCTCAAGAGGCTCTTCGGTAAGT
TCGGGCCCGCCCTCAGCGTCAAAGTCATGACGGACGAGAGCGGCACGTCCAAAGGCTTCGGCTTTGTGAACTTCGAGAGG
CACGAGGACGCCCAGAAGGCCGTGGAGGAGATGAACGGCAAGGAGCTGAACGGGAAGAAGATCTACGTGGGCCGGGCTCA
GAAAAAGGTCGAGCGCCAGACGGAACTCAAGCGCAAGTTCGAGCAGATGAAGCAGGACCGCATCACCAGGTACCAGGGGG
TGAACCTGTACGTGAAGAATCTGGACGACGGCATCGACGACGAGCGCCTGCGCAAAGAGTTCTCCCCCTTCGGGACCATC
ACCAGCGCCAAGGTGATGATGGAAGGGGGCCGCAGCAAAGGCTTCGGCTTCGTCTGCTTCTCCTCCCCCGAGGAGGCCAC
CAAAGCCGTCACGGAGATGAACGGCCGGATCGTGGCCACCAAGCCCCTGTACATAGCCTTGGCCCAGCGCAAAGAGGAGC
GGCAGGCCCACCTCACGAACCAGTACATGCAGAGGATGGCCAGCGTCCGGGCCGTGCCCAACCCCGTGATCAACCCTTAC
CAGCCTCCCTCGGGCTACTTCATGGCGGCCATCCCCCAGGCGCAGAACCGCCCCGCCTACTATCCCCCCGGCCAGATCGC
CCCTCTCAGACCCAGTCCCCGGTGGACGGCCCAGGGGGCCAGGCCTCATCCGTTCCAAAACATGCCCGGGGCCATCCGGC
CGGCGGCTCCCAGGCCCCCGTTCGGGACCATGAGGCCGTCTTCCTCGCAGGTGCCAAGGGCCATGTCCTCCCGGGTCTCC
AACGCCACCTCGCAGAGCATGGGCCCCCGCGCGGCCGCGGGGTCCGCCTCCGCGGGGACCCCAGCCGTGCGTTCGGCGCC
CCAGTACAAGTACGCCGCTGGCGTGCGCAATCCCCAGCAGCACCTGAACCCGCCGCCTCAGGTGACCCTGCAGCAGCCCG
CCGTCCACGTGCAGGGTCAGGAGCCGCTCACGGCTTCCATGTTGGCCGCCGCCCCTCCACAGGAGCAGAAGCAGATGCTG
GGAGAACGGCTGTTCCCGCTCATCCAGGCCATGCACCCGACCCTGGCCGGTAAGATCACTGGCATGTTGCTGGAGATCGA
CAACTCGGAGCTTCTCCACATGCTCGAGTCCCCGGAGTCTCTGCGGTCCAAGGTCGACGAAGCGGTGGCGGTGCTGCAAG
CTCACCAGGCGAAAGAGGCCGCCCAGAAAGCGGTCAACAGTGCTCCCGACGTGCCTCCTGTCTAA

ORF - retro_shar_24 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.53 %
Parental protein coverage: 94.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL
AL.DTFSAFGNILSCKVVCDENGSKGYGFVHFET.EAAERAI.KMNGMLLNDRKVFVGRFKSRKEREAEL
RetrocopyALFDTFSAFGNILSCKVVCDENGSKGYGFVHFETREAAERAIDKMNGMLLNDRKVFVGRFKSRKEREAEL
ParentalGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNG
GARAKEFTNVYIKNFGEDMDD.RLK.LFGKFGPALSVKVMTDESG.SKGFGFV.FERHEDAQKAV.EMNG
RetrocopyGARAKEFTNVYIKNFGEDMDDLRLKRLFGKFGPALSVKVMTDESGTSKGFGFVNFERHEDAQKAVEEMNG
ParentalKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSA
KELNGK.IYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSA
RetrocopyKELNGKKIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSA
ParentalKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVP
KVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY.ALAQRKEERQAHLTNQYMQRMASVRAVP
RetrocopyKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYIALAQRKEERQAHLTNQYMQRMASVRAVP
ParentalNPVINPYQPPSGYFMAAIPQTQNRAAYYPASQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFST
NPVINPYQPPSGYFMAAIPQ.QNR.AYYP..QIA.LRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPF.T
RetrocopyNPVINPYQPPSGYFMAAIPQAQNRPAYYPPGQIAPLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFGT
ParentalMRPASSQVPRVMSTQRVANTSTQTMGPRPAA-AAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQ
MRP.SSQVPR.MS..RV.N...Q.MGPR.AA..A.A.TPAVR..PQYKYAAGVRNPQQHLN..PQVT.QQ
RetrocopyMRPSSSQVPRAMSS-RVSNATSQSMGPRAAAGSASAGTPAVRSAPQYKYAAGVRNPQQHLNPPPQVTLQQ
ParentalPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLR
PAVHVQGQEPLTASMLA.APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLR
RetrocopyPAVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLR
ParentalSKVDEAVAVLQAHQAKEAAQKAVNSATGVPTV
SKVDEAVAVLQAHQAKEAAQKAVNSA..VP.V
RetrocopySKVDEAVAVLQAHQAKEAAQKAVNSAPDVPPV

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_24 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 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Callithrix jacchus ENSCJAG000000158335 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
Dasypus novemcinctus ENSDNOG000000087182 retrocopies
retro_dnov_1530, retro_dnov_2259,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Gorilla gorilla ENSGGOG000000067851 retrocopy
retro_ggor_1986,
Myotis lucifugus ENSMLUG000000122451 retrocopy
retro_mluc_579,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG00000011267 1 retrocopy
retro_shar_24 ,
Sarcophilus harrisii ENSSHAG000000138321 retrocopy
retro_shar_78,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus ENSSTOG000000163952 retrocopies
retro_itri_139, retro_itri_48,
Tarsius syrichta ENSTSYG000000042292 retrocopies
retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,




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