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 symbol: None
• Ensembl ID: PGSC0003DMG400014862
• Aliases: None
• Description: None

Sequence

>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

Alignment

ORF - retro_stub_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.26 %
• Parental protein coverage: 100. %
• 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

Expression

RNA-Seq

Solanum tuberosum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum tuberosum was not studied using ChIP-Seq data.

EST

Solanum tuberosum was not studied using EST data.

TSS

Solanum tuberosum was not studied using FANTOM5 data.

Lab

retro_stub_9 was not experimentally validated.

Homology

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.

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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	retro_slyc_26,