RetrogeneDB ID: retro_stub_19

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 9:8918339..8920175(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400040591
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400029083
• Aliases: None
• Description: None

Sequence

>retro_stub_19
CGAGTGTATTCAATGGAGGATATAAGCTCTCACTATTGTATTAACAGTGGTATTCTTCCTTCTCTTGGCGGCCATAGTGA
TAGCAAAATTAGGCTTCGTAACTACATCATCTCCCCTACTAATCCCCGTTACAAGGTTTGGGACGCATTTTTGGTGCTTC
TTGTTTTCTACACAGCATGGGCATCACCTTTTCAGATTGGATTTCTAGAAACACCTCAAGGACTTATTGCCATCTTAGAT
AACATAGTCAACTTCTTTTTTGCCATTGACATTATCCTCTCATTGTTCTTTGTTGCATATCTTGATAAATCAACTTACAC
TATGATTGATGACCCAAAGCGCATTGCTTTGAGGTATATAAAATATGGATTTATCTTTGATTTCATATCCACTATCCCTT
ACGAAGCATTGCCTCGTATTCTTCAATCATATGGATTCTTGAGTATGCTTCGTCTCTGGCGTCTCAGAAGAGTCAGTGCC
ATGTTTGTCGAATTGGAGAAAAACAACAAGTTGAGTTACTTTGGGATTCGAGTACTCAAGCTTGTATGTGTCACTCTTTT
TGCTGTTCATTCTGCTGGCTGCTTCTACTACTTTCTTGCTGCTCGGATTAAAGACGTTAGTAAAACATGGCTTTCACTGG
GAAATCTTCATGATAGGAGTATCTGGGATCTTTATGTAATGTCTATGTATTGGTCCATTACAACTCTTACAACAACTGGC
TATGGGGATTTGCATGCTGTCACTACAGAGGAAATGATATTCACCATGGTTTACATGTTATTCGACCTCGGGCTGACTGC
ATATCTTATTGGAAACATGACCAACTTGGTTGTCCATGGAACCAATAAGACGCAGAAATTTAGGGATGCTATTCAAGCTG
CCTCAAGCTTTGCACAAAGGAATAATCTGCCTGTTCGACTTGAAGAACAGATGCTAGATCACTTGTCAATGATGCACAGA
ACAGATACGGAAGGTCTGCAGCAGCAAGAAACTCTTGAAACACTACCCAGAGCTATTCGATCTGCCATTTCACATCATCT
ATTCTATTCACTGGTGGATAAGGCCTACTTATTCCAGGGGATATCAAATGACTTACTTTTTCAACTGATTTCTGAGATGA
AGGCCGAGTATTTCCCTCCAAAAGAGGATGTCATTTTGCAAAATGAAGCATCAACAGAACTCTACATCCTCGTAACTGGA
GCAGTGGATCTTATATCACACAAGAATGGTATGGATCATGTAGTTGGCGAGTTGAAGGCAGGGGATGTTTGCGGAGAAGT
TGGTATCCTTTGTTGTAGGCCTCAACTTTTTACTGTTCGAACCAAAAGAATATCCCAACTGCTACGCCTGGATCGTACTT
CATTTTTCAACACCGTTAAAGCAAATAAAGGAGACAGGACAATAATTATGAACAATCTCCTTCAGCATTTGAAAGAGCAA
ACAGACCCAATGATGACTGCAGTATTAGCAGATATAGAACATATCTTCACTCCTGAAGAAACAACATCAGTAGCTAGCGA
AAATGGTTCGTCCAATGCCAGATTGAGAAGAAGGGCTAATTTCTTTCGGAATTCACTGATAGGTCCAGAATATTCTTCAG
CTAAAATTGGAAATTCAAGAATTCCAGGCAGAATAACCATCGGTTGTCTACAGAAAGCTGATATGCGTAGAAGAGTTGTG
CCTTTGCCGGATTCCATACAAGAGCTACTTGATATCGGTGCTGAGAAATTTGGCATCTCTCTCACTGAAGTACTAACTGA
AGATGGAGCACTTATTGAGGACATTGCACTGATAAGAGATGGAGATCATCTAGTTCTTGCTACTTCAGAAAATTAA

Alignment

ORF - retro_stub_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.92 %
• Parental protein coverage: 58.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAYSMDDKSSHYSITSAILPSLGAHTNCKTKLRRYIISPSNPRYRAWNAYLVLLVFYTAWASPFQFGFLD
          R.YSM.D.SSHY.I.S.ILPSLG.H...K..LR.YIISP.NPRY..W.A.LVLLVFYTAWASPFQ.GFL.
Retrocopy RVYSMEDISSHYCINSGILPSLGGHSDSKIRLRNYIISPTNPRYKVWDAFLVLLVFYTAWASPFQIGFLE

Parental  RPRGVIPILDNIANSFFAIDIVLT-FFVAYLDKSACSMIDDPKRIALRYTKSGFLFDVISTIPSELIRKS
          .P.G.I.ILDNI.N.FFAIDI.L..FFVAYLDKS...MIDDPKRIALRY.K.GF.FD.ISTIP.E.....
Retrocopy TPQGLIAILDNIVNFFFAIDIILSLFFVAYLDKSTYTMIDDPKRIALRYIKYGFIFDFISTIPYEAL---

Parental  TPYFLQSYEYFSILRLWRLRRVSAMFARLEKNRKISYFGVRVLKLICVTLFAVHCAGCFYYFLAARKQDT
          .P..LQSY...S.LRLWRLRRVSAMF..LEKN.K.SYFG.RVLKL.CVTLFAVH.AGCFYYFLAAR..D.
Retrocopy -PRILQSYGFLSMLRLWRLRRVSAMFVELEKNNKLSYFGIRVLKLVCVTLFAVHSAGCFYYFLAARIKDV

Parental  SKTWLSLAIGNHHDRSIWDLYVMCMYWSITTLTTTGYGDLHAVATEEMIFTMFYMLFDLGLTAYLIGNMT
          SKTWLSL..GN.HDRSIWDLYVM.MYWSITTLTTTGYGDLHAV.TEEMIFTM.YMLFDLGLTAYLIGNMT
Retrocopy SKTWLSL--GNLHDRSIWDLYVMSMYWSITTLTTTGYGDLHAVTTEEMIFTMVYMLFDLGLTAYLIGNMT

Parental  NLVVHGTSKTRKFRDTIQAASSFAQRNKLPVRLEEQMIAHLRLRHRTDSEGLQQQETLETLPKAIRSGIS
          NLVVHGT.KT.KFRD.IQAASSFAQRN.LPVRLEEQM..HL...HRTD.EGLQQQETLETLP.AIRS.IS
Retrocopy NLVVHGTNKTQKFRDAIQAASSFAQRNNLPVRLEEQMLDHLSMMHRTDTEGLQQQETLETLPRAIRSAIS

Parental  HYLFYPLVDKVYLFHGVSNDLLFQLVSEMKAEYFPPKEDVILQNEAPTDLYILVTGAVDLISHKNGMDQV
          H.LFY.LVDK.YLF.G.SNDLLFQL.SEMKAEYFPPKEDVILQNEA.T.LYILVTGAVDLISHKNGMD.V
Retrocopy HHLFYSLVDKAYLFQGISNDLLFQLISEMKAEYFPPKEDVILQNEASTELYILVTGAVDLISHKNGMDHV

Parental  VGELKMGDVCGEVGVLCCRPQLFNVRTKKVSQLLRLDRSSFFNIVKTNIGDGTIIMNNLLQHLKERRDPM
          VGELK.GDVCGEVG.LCCRPQLF.VRTK..SQLLRLDR.SFFN.VK.N.GD.TIIMNNLLQHLKE..DPM
Retrocopy VGELKAGDVCGEVGILCCRPQLFTVRTKRISQLLRLDRTSFFNTVKANKGDRTIIMNNLLQHLKEQTDPM

Parental  MTAILADIEHMLT
          MTA.LADIEH..T
Retrocopy MTAVLADIEHIFT

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_19 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400029083	1 retrocopy	retro_stub_19 ,