RetrogeneDB ID: | retro_shar_773 | ||
Retrocopy location | Organism: | Tasmanian devil (Sarcophilus harrisii) | |
| Coordinates: | GL864774.1:2708950..2709828(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSHAG00000017421 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TAF15 | ||
| Ensembl ID: | ENSSHAG00000003105 | ||
| Aliases: | None | ||
| Description: | TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa [Source:HGNC Symbol;Acc:11547] |
Retrocopy-Parental alignment summary:
>retro_shar_773
TATGACCAACACCAAGGTTCATATGATGAGCAATCAAATCATGATCAGCAGCAAGACTCATATAATCAAAATCAGCAGTC
CTATCACTCACAAAGGGAAAGTTACAGCCACCATACACAAGATGACCATCGTGACATGAGTAGGTATGGAAAAGATAATA
GAAGATATGGTGGGTCACAGGGAGGAGGTAGAGAACATGGGAGATATGACAAGGATGGAAGAGGTCTATGACAGGATCAA
GTGGTGGTGACTGTGGTGGCTTCAAAAATATTGGTGGCCACAGGGATTATGGACCGAAAACAGATGCTGACTCCAGAGTC
TGATAATTCAGACAACACGATCTTTGTTGAAGGACTTGGAGAAGGGGTATCAACTGATCAAGTTGGAGACTTCTTTAAGC
AAATAGGAATTATTAAGACAAATCAGAAGACTGGTGAACCGATGATTAAATCTATATACAGACAAGGGTACAGGCAAGCC
AAAAGGAGAGGCAACAATGCCATTTGATGACCCTCCTTCAGCTAAAGCTGCAATTGATGGCTTGATGGAAAAGAATTCCA
TGAAAATATCATCAAAGTATCTTTTGCCACTAGAAGACCTGAATTCCTGAGAGGGGGTGGAAGTGGAAGTGGGGGATGAG
GTTCATGTGGAGGATACAAAGGGCTTGGAGGCTTTCAAGGTAGAGGAAATGACTTGAAAAGTGGTGACTGGATTTGTCCT
AATCTGTCATGTGGAAACATGAACTTTGCCCAAAGGAATTCCTGTAATCAGTGTAATGACCCCAGACCACAGGACTCTCG
TCCTTCAGTAGGAGATTTCTGAGGGAGAGGCTATGGTGGCAAGAGGGGCTATACAGGCAGGGTGGCAGAGGTGGAGAC
ORF - retro_shar_773 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.29 % |
| Parental protein coverage: | 53.75 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | YDQHQGSYDEQSNYDQQQDSYNQNQQSYHSQRESYSHHTQDDRRDMSRYGEDNRGYGGSQGGGRGRGGYD |
| YDQHQGSYDEQSN.DQQQDSYNQNQQSYHSQRESYSHHTQDD.RDMSRYG.DNR.YGGSQGGGR..G.YD | |
| Retrocopy | YDQHQGSYDEQSNHDQQQDSYNQNQQSYHSQRESYSHHTQDDHRDMSRYGKDNRRYGGSQGGGREHGRYD |
| Parental | KDGRG-PMTGSSGGDRGGFKNFGGHRDYGPKTDADS-ESDNSDNNTIFVQGLGEGVSTDQVGDFFKQIGI |
| KDGRG..MTGSSGGD.GGFKN.GGHRDYGPKTDADS.ESDNSD.NTIFV.GLGEGVSTDQVGDFFKQIGI | |
| Retrocopy | KDGRG<SMTGSSGGDCGGFKNIGGHRDYGPKTDADS>ESDNSD-NTIFVEGLGEGVSTDQVGDFFKQIGI |
| Parental | IKTNKKTGKPMI-NLYTDKDTGKPKGEATVSFDDPPSAKAAID-WFDGKEFHGNIIKVSFATRRPEFLRG |
| IKTN.KTG.PMI.NLYTDK.TGKPKGEAT..FDDPPSAKAAID.W.DGKEFH.NIIKVSFATRRPEFLRG | |
| Retrocopy | IKTNQKTGEPMI>NLYTDKGTGKPKGEATMPFDDPPSAKAAID<WLDGKEFHENIIKVSFATRRPEFLRG |
| Parental | GGSGGGRRGSRGGYRGRGGFQGRGGDPKSGDWVCPNPSCGNMNFARRNSCNQCNEPRPEDSRPSGGDFRG |
| GGSG.G..GS.GGY.G.GGFQGRG.D.KSGDW.CPN.SCGNMNFA.RNSCNQCN.PRP.DSRPS.GDF.G | |
| Retrocopy | GGSGSGG*GSCGGYKGLGGFQGRGNDLKSGDWICPNLSCGNMNFAQRNSCNQCNDPRPQDSRPSVGDF*G |
| Parental | RGYGGERGYRGR-GGRGGD |
| RGYGG.RGY.GR.GGRGGD | |
| Retrocopy | RGYGGKRGYTGR<GGRGGD |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Sarcophilus harrisii was not studied using RNA-Seq expression data.
Sarcophilus harrisii was not studied using ChIP-Seq data.
Sarcophilus harrisii was not studied using EST data.
Sarcophilus harrisii was not studied using FANTOM5 data.
retro_shar_773 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sarcophilus harrisii | ENSSHAG00000003105 | 1 retrocopy |
retro_shar_773 ,
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