RetrogeneDB ID: | retro_stub_9 | ||
Retrocopy location | Organism: | Potato (Solanum tuberosum) | |
| Coordinates: | 4:67293401..67295702(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | PGSC0003DMG400021513 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | PGSC0003DMG400014862 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_stub_9
ATGGAAAGACTCGGGATCGTGTTTCTTTCTACACTAGTGCTAGTGTTGTTTCATGTGTTTGTTGATGCAAGCCAGAACCA
AAAGAAGACTTACATAATTCACATGGACAAGTTCAACATGCCTGCTGATTTTGATGATCATACTCAGTGGTATGACTCAT
CGTTGAAGTCAGTATCCAAGAGTGCCAATGTGCTTTACACCTACAACAGTGTCATCCATGGCTATTCAACACAGCTAACA
GCTGATGAAGCCAAAGCACTTGAACAGCAACCAGGAATTCTCTCGGTCCACGAGGAAGTGATATACGAGCTTCACACCAC
TCGATCCCCTACGTTTCTGGGACTTGAAGGGCACGAAAGTAGATCATTCTTTCCTCAGACTGAAGCAAGGAGTGAGGTCA
TTATTGGTGTGCTGGACACAGGTGTTTGGCCTGAATCGAAAAGTTTTGATGACACTGGACTAGGTCCAGTCCCTGCAAGC
TGGAAGGGCAAGTGTCAAACTGGCAAGAACTTCGACGCATCAAGCTGTAATCGGAAACTCATTGGTGCGAGGTTTTTCTC
ACAAGGTTATGAAGCAGCTTTTGGGGCAATCGATGAGACCATCGAATCCAAGTCACCAAGGGACGATGAAGGCCATGGCA
CACACACTGCAACTACAGCAGCTGGCTCAGTTGTAACCGGAGCTAGCCTCTTGGGTTATGCCACTGGTACAGCACGTGGG
ATGGCTTCACACGCAAGAGTGGCTGCATACAAGGTATGTTGGACCGGAGGATGTTTTAGCAGCGACATACTTGCAGGGAT
GGACCAGGCTGTCATAGATGGTGTAAATGTGCTCTCACTGTCCCTTGGTGGCACAATTTCTGATTATCATAGGGACATAG
TTGCAATTGGAGCATTTTCTGCAGCTTCTCAAGGAATCTTTGTTTCATGCTCAGCGGGGAATGGCGGTCCAAGCTCTGGG
ACCCTATCCAACGTTGCACCATGGATAACTACTGTAGGTGCAGGAACCATGGACCGTGAATTTCCAGCATACATTGGCAT
TGGAAATGGGGAAAAACTCAATGGAGTATCACTTTACAGTGGAAAGGCATTGCTTAGTTCTGTGATGCCACTGGTGTATG
CTGGAAATGTCAGCCAATCATCAAATGGAAATTTATGCACAAGTGGTAGTCTAATTCCGGAAAAAGTTGCTGGGAAAATT
GTCGTATGTGACCGAGGGATGAATGCAAGGGCACAAAAGGGTTTGGTTGTGAAGGATGCTGGTGGAATAGGGATGATTCT
GGCAAACACAGACACTTATGGAGATGAGTTGGTTGCTGATGCACACCTCATACCTACAGCTGCAGTTGGTCAAACTGCTG
GCAACTTGATCAAGCAGTACATAGCTTCTAACAGTAATCCAACTGCCACAATTGCATTTGGAGGTACCAAGTTGGGTGTT
CAACCATCGCCAGTTGTTGCAGCTTTTAGTTCCAGAGGGCCAAACCCAATCACACCAGATATACTCAAACCTGATTTGAT
AGCACCAGGTGTCAACATTCTTGCTGGTTGGACAGGGAAAGTTGGACCAACTGGCTTGCAAGAAGACACCAGGAATGTAG
GCTTCAACATCATCTCTGGAACTTCCATGTCATGTCCCCATGTAAGTGGGCTAGCAGCACTACTCAAAGCTGCCCATCCA
GAATGGAGTCCAGCAGCTATAAGGTCAGCACTGATGACTACAAGTTACAGCACATACAAAAATGGAAAAACAATTGAGGA
TGTAGCAACAGGAATGTCATCTACACCATTTGATTATGGTGCTGGACATGTGAATCCAACAGCAGCTGTCAATCCTGGTT
TAGTGTATGATCTAACAGTTGATGACTATATAAACTTCCTATGTGCCTTGGACTACAGCCCGAGTATGATCAAGGTCATT
GCAAAGAGAGACATCTCCTGTGACAAAAATAAGGAGTATAGAGTTGCTGATCTTAATTACCCATCTTTTTCCATTCCTAT
GGAAACGGCCTGGGGTGAACATGCAGATAGTAGTACACCCACCGTGACCAGATACACAAGGACTCTAACAAATGTGGGAA
ACCCAGCTACATACAAGGCCTCAGTCTCTTCTGAAACACAGGAAGTGAAGATTCTGGTTGAGCCACAAACACTTACTTTC
AGCCGAAAGAACGAAAAGAAAACCTACACTGTGACCTTCACTGCTAGTTCCAAGCCATCAGGCACAACTAGCTTCGCTCG
ACTGGAGTGGTCAGATGGACAACACGTTGTTGCTAGCCCAATTGCTTTCAGCTGGACATGA
ORF - retro_stub_9 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.26 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKSQMPEGFEDHTHWYDSSLRSVSASAEMLYVYNNAVHGFAARLTPEEAESLQNQPGILSVLPEMKYEL |
| M.K..MP..F.DHT.WYDSSL.SVS.SA..LY.YN...HG....LT..EA..L..QPGILSV..E..YEL | |
| Retrocopy | MDKFNMPADFDDHTQWYDSSLKSVSKSANVLYTYNSVIHGYSTQLTADEAKALEQQPGILSVHEEVIYEL |
| Parental | HTTRTPLFLGLD--VSADYFPESNAMGDVIVGVLDTGVWPESKSFDDNGFGPIPASWKGECESGTNFTSK |
| HTTR.P.FLGL....S...FP...A...VI.GVLDTGVWPESKSFDD.G.GP.PASWKG.C..G.NF... | |
| Retrocopy | HTTRSPTFLGLEGHESRSFFPQTEARSEVIIGVLDTGVWPESKSFDDTGLGPVPASWKGKCQTGKNFDAS |
| Parental | NCNRKLIGARYFAKGYESTLGPIDVSKESKSPRDDDGHGTHTSTTAAGSVVQGASLLGYASGNARGMATH |
| .CNRKLIGAR.F..GYE...G.ID...ESKSPRDD.GHGTHT.TTAAGSVV.GASLLGYA.G.ARGMA.H | |
| Retrocopy | SCNRKLIGARFFSQGYEAAFGAIDETIESKSPRDDEGHGTHTATTAAGSVVTGASLLGYATGTARGMASH |
| Parental | ARVAVYKVCWVGGCFSSDILAGLDKAIDDNVNVLSLSLGGGNSDYYRDSIAIGAFAAMEKGILVSCSAGN |
| ARVA.YKVCW.GGCFSSDILAG.D.A..D.VNVLSLSLGG..SDY.RD..AIGAF.A...GI.VSCSAGN | |
| Retrocopy | ARVAAYKVCWTGGCFSSDILAGMDQAVIDGVNVLSLSLGGTISDYHRDIVAIGAFSAASQGIFVSCSAGN |
| Parental | AGPSPYSLSNVAPWITTVGAGTLDRDFPAYVSLGNGKNFSGVSLYKGDSSLSKMLPFVYAGNASNMTNGN |
| .GPS...LSNVAPWITTVGAGT.DR.FPAY...GNG....GVSLY.G...LS...P.VYAGN.S...NGN | |
| Retrocopy | GGPSSGTLSNVAPWITTVGAGTMDREFPAYIGIGNGEKLNGVSLYSGKALLSSVMPLVYAGNVSQSSNGN |
| Parental | LCMTGTLIPEEVKGKIVLCDRGINPRVQKGSVVKAAGGAGMVLANTAANGDELIADAHLIPATSVGQTTG |
| LC..G.LIPE.V.GKIV.CDRG.N.R.QKG.VVK.AGG.GM.LANT...GDEL.ADAHLIP...VGQT.G | |
| Retrocopy | LCTSGSLIPEKVAGKIVVCDRGMNARAQKGLVVKDAGGIGMILANTDTYGDELVADAHLIPTAAVGQTAG |
| Parental | EAIKKYLTSDPNPTATILFEGTKVGIKPSPVVAAFSSRGPNSITQEILKPDIIAPGVNILAGWTGAAGPT |
| ..IK.Y..S..NPTATI.F.GTK.G..PSPVVAAFSSRGPN.IT..ILKPD.IAPGVNILAGWTG..GPT | |
| Retrocopy | NLIKQYIASNSNPTATIAFGGTKLGVQPSPVVAAFSSRGPNPITPDILKPDLIAPGVNILAGWTGKVGPT |
| Parental | GLAEDDRRVEFNIISGTSMSCPHVSGLAALLKGAHPDWSPAAIRSALMTTAYTVYKKGGALQDVVTGKPS |
| GL.ED.R.V.FNIISGTSMSCPHVSGLAALLK.AHP.WSPAAIRSALMTT.Y..YK.G....DV.TG..S | |
| Retrocopy | GLQEDTRNVGFNIISGTSMSCPHVSGLAALLKAAHPEWSPAAIRSALMTTSYSTYKNGKTIEDVATGMSS |
| Parental | TPFDHGAGHVDPVAALNPGLVYDLKADDYLNFLCALNYTSIQINSVARRPFSCETSKKFSVADLNYPSFA |
| TPFD.GAGHV.P.AA.NPGLVYDL..DDY.NFLCAL.Y....I...A.R..SC...K...VADLNYPSF. | |
| Retrocopy | TPFDYGAGHVNPTAAVNPGLVYDLTVDDYINFLCALDYSPSMIKVIAKRDISCDKNKEYRVADLNYPSFS |
| Parental | VVFPEQMTASSGSGSSSI-KHTRTLTNVGPAGTYKVNVISPSNSVKVVVEPEILAFTRMNEQKSYTVTFT |
| ............S........TRTLTNVG...TYK..V.S....VK..VEP..L.F.R.NE.K.YTVTFT | |
| Retrocopy | IPMETAWGEHADSSTPTVTRYTRTLTNVGNPATYKASVSSETQEVKILVEPQTLTFSRKNEKKTYTVTFT |
| Parental | APSMPSTENVYARIEWSDGKHIVSSPVAISWT |
| A.S.PS.....AR.EWSDG.H.V.SP.A.SWT | |
| Retrocopy | ASSKPSGTTSFARLEWSDGQHVVASPIAFSWT |
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_9 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Solanum tuberosum | PGSC0003DMG400014862 | 2 retrocopies |
retro_stub_57, retro_stub_9 ,
|
| Solanum lycopersicum | Solyc03g044150.2 | 1 retrocopy |