RetrogeneDB ID: | retro_stub_144 | ||
Retrocopy location | Organism: | Potato (Solanum tuberosum) | |
| Coordinates: | 8:16132633..16133563(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | PGSC0003DMG400025528 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_stub_144
ATGGGAGGAAGTCCAGTCACTGATTATTGGGAGTGTATTGCAAATGACGCTCAGAAACTACATATGATTGGGTGTATAGG
TGAAGGAAAAAGTACCACAGGCAATAACATTCTTGGTAGAAATGTATTCCAGTTGAGGTCTAGCTCTGGTGGTGTTGCAA
GAACTTTTGGAATTCAGAGGACTCGATTAAAGGATGGGCAGATTCTTGATGTGATCGATACCCCTAGATTTGATTTTAAT
GCTGAATCTGGATTAGTTTGAAATGAAATTCGTAAATGCATTGATTTGGCCGATGATGGTGTCCACGTTGTTCTTTTTGT
TGTCTGTACGAACTAGATTTTCAAAAGAAGAACAGGCTGCTATCCAGTACTTTAAGAAGCTCTTTGGGACCAAAATTAGT
GATTACGTAATTGTGGTCTAAACTGGAGGGGATAAGCTAGAAGATAATGACTCTTTGAATGATCACTTAGATTGTTCCTG
CCCTGAGCATTTAAAGGAAGTTCTTAAGATGTGTGGGAATAGACGGTGCTTTTCGATAATAAAACTGAAGAACCAGCGAA
GAAAGCTGAACAATTGAGGGAATTTCTTTTCCATGTGAATATGGTTGTACAAATGACTAGTGGAAAATCATATACGAGTG
AATTATTTGAGGAAGTAAAGAAGATGAAGCTTCATAATGACTCATTGGAGGTTAGTTCTTTGCTCGGAGATTTAAAGCAA
GAGGTAGGTGAGTTAAAGGAACAACTGCAGAGGTTCTCTTTCAAGGAGGAACACAGGTGAATAACTGAAATGGTTGAATC
TAAGATGTACAATACCATGCATAGTCTTGAAAAGCAGTTGGAGGAGGTGCGTACTGCTCGGTCAGAGGTAGAAAGCAAAA
TTCGTGAATTGAAAGATAGCTTAGAGAAAGTTCAAAGAGAGACTGAGGAG
ORF - retro_stub_144 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.42 % |
| Parental protein coverage: | 92.9 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MGGSAISDDWEFTTTGARTLVLVGCTGNGKSATGNSIVGRKAFKSMSSSAGVTSTCELQRTVLEDNQILD |
| MGGS...D.WE.....A..L...GC.G.GKS.TGN.I.GR..F...SSS.GV..T...QRT.L.D.QILD | |
| Retrocopy | MGGSPVTDYWECIANDAQKLHMIGCIGEGKSTTGNNILGRNVFQLRSSSGGVARTFGIQRTRLKDGQILD |
| Parental | VIDTPGLFDCSSEPEFVGNEIVKCINMAKDGIHAVLVVLSVRSRFSR-EEHAAVQSLREFFGSKISDYMI |
| VIDTP..FD...E...V.NEI.KCI..A.DG.H.VL.V......F.R.E..A..Q.....FG.KISDY.I | |
| Retrocopy | VIDTP-RFDFNAESGLV*NEIRKCIDLADDGVHVVLFVVCTN*IFKR>EQAA-IQYFKKLFGTKISDYVI |
| Parental | LVFTGGDDLEDNDETLDDYLGRDCPELLKNTLKMCGNRQ-VLFDNKTKDPLKKAEQLKQLLFLVNVVVEN |
| .V.TGGD.LEDND..L.D.L...CPE.LK..LKMCGNR..VLFDNKT..P.KKAEQL...LF.VN.VV.. | |
| Retrocopy | VV*TGGDKLEDND-SLNDHLDCSCPEHLKEVLKMCGNRR<VLFDNKTEEPAKKAEQLREFLFHVNMVVQM |
| Parental | NAGKPYTDDLFKELKKGATKLHNQATEVNFLVGYTKQERLELKEQMQK-SYEEQLKRITEVVESKLKETT |
| ..GK.YT..LF.E.KK...KLHN...EV..L.G..KQE..ELKEQ.Q..S..E....ITE.VESK...T. | |
| Retrocopy | TSGKSYTSELFEEVKK--MKLHNDSLEVSSLLGDLKQEVGELKEQLQRFSFKEEHR*ITEMVESKMYNTM |
| Parental | HRLEEQLAKEQAARLKSELSAKNAQKKSDEEIRKLRE |
| H.LE.QL.....AR...E..............R...E | |
| Retrocopy | HSLEKQLEEVRTARSEVESKIRELKDSLEKVQRETEE |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Solanum tuberosum was not studied using RNA-Seq expression data.
Solanum tuberosum was not studied using ChIP-Seq data.
Solanum tuberosum was not studied using EST data.
Solanum tuberosum was not studied using FANTOM5 data.
retro_stub_144 was not experimentally validated.
Retrocopy orthology:
Solanum tuberosum 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Solanum tuberosum | PGSC0003DMG400025528 | 2 retrocopies |
retro_stub_139, retro_stub_144 ,
|