RetrogeneDB ID: retro_stub_122

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 5:30262248..30263198(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400044937
• Aliases: None
• Description: None

Sequence

>retro_stub_122
AAGTTTGCATAATTGGTCAAGATGGAAGACTTCACAGAGGAAGGTGTAAAATCTAGGAAAATTCAGTCTATGGGTTCATT
GCAAGCTGGAAGTAGGGCCATACAATCGGGTGCAATTTGCGGCATAAAGAACAAAAGGGAGGATGTGTCAAATGTCACTT
CCCCATAGGGAGGACCATCCCACCGATACCCCCAACAACCCACAAATTATTGCACATACTTTATACGTCCATACCAAGTA
TATAATACCCAACAACACTATAATCCAACTCGAGCACCAGCACACCAAAATCCACCAAGACCATATTTCCCTATCCAAGC
ACTAATCCACAAAAATAGACCAGTATATGCACCAAGACATCTCAAAGCTAGAAATCCTTGCGCTTACACACCCATTGTCG
AGACTTATGCCCAATTTTTTGAGAGGTTGAGGACAGCGGGAGTGTTGCAACAAGTTGAAGGAAAACCTCCTGATCCAGTG
CCTCGCAACTTCAATGGAAACAAGTGATACACTTATCACTCGGGAATTCACGGACATAACATAGAAGATTGCTATGGTTT
GAAGGGCCAAATCGAGTCTTTCATCAAGAGAGGGGTAATCAAATTTACTCCAACACCTCCTAATGTAAACAATAACCCTT
TGCCCAACCACGCGAATCGAACAGTCAACATGGTTACTCTAGATGAGAATATGAGTGCTCCGACTATCCAAACATAGATG
AACCAGATGCCATGACATCTTCGCAGCAACCTGTTATCACTTTTCCATTAAGGGAATCTCTGACTGTTCAAATATATACC
GTGAGAGGTATAGTGACCACTCTAATTGCTAGAAATCCTGAGTATGACTCCAAAGTAGTCCCATGGGACTATCGAGCAGG
TGCCAAGGGCAAGATGATATATATTGCCGTGGCTCAATGGATGACTAGATTGGGAAGGTGTTATTCCCCA

Alignment

ORF - retro_stub_122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.18 %
• Parental protein coverage: 60.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QYAEMEKDTQLKEDASINAQLQVYGRLQTASRAIQAGSIGGIKKKNEDVSAVTYQQGGPSHRYP-SNPQI
          ..A...K.....E........Q..G.LQ..SRAIQ.G.I.GIK.K.EDVS.VT...GGPSHRYP..NPQI
Retrocopy KFA*LVKMEDFTEEGVKSRKIQSMGSLQAGSRAIQSGAICGIKNKREDVSNVTSP*GGPSHRYP>NNPQI

Parental  AAHTSYV-PYPVYNTQPHYNPPRAPAYQNPPRPYVPVQAQIHQNRPAYAPRPRPNFKARNARTYTPIAES
          .AHT.YV.PY.VYNTQ.HYNP.RAPA.QNPPRPY.P.QA.IH.NRP.YAPR.....KARN...YTPI.E.
Retrocopy IAHTLYV<PYQVYNTQQHYNPTRAPAHQNPPRPYFPIQALIHKNRPVYAPR---HLKARNPCAYTPIVET

Parental  YAQLFERLRTAGVLQPVQGKLPDPIPRNFDGNKQYAYHSGIQGHDTEDCYGLKNQIESLIKRGVIKCTPA
          YAQ.FERLRTAGVLQ.V.GK.PDP.PRNF.GNK.Y.YHSGI.GH..EDCYGLK.QIES.IKRGVIK.TP.
Retrocopy YAQFFERLRTAGVLQQVEGKPPDPVPRNFNGNK*YTYHSGIHGHNIEDCYGLKGQIESFIKRGVIKFTPT

Parental  PPNVNNNPLPNHENRKVNMVTLDE-EYRGPDCPDIDEPDAMTSSVQPVITVQLREPLTVQTYLPRVVVTT
          PPNVNNNPLPNH.NR.VNMVTLDE.EY...D.P.IDEPDAMTSS.QPVIT..LRE.LTVQ.Y..R..VTT
Retrocopy PPNVNNNPLPNHANRTVNMVTLDE<EYECSDYPNIDEPDAMTSSQQPVITFPLRESLTVQIYTVRGIVTT

Parental  LIARKPEYDTKAVPWDYRADAKGKMIDTTLKHQRGTNGFGYEP
          LIAR.PEYD.K.VPWDYRA.AKGKMI...........G..Y.P
Retrocopy LIARNPEYDSKVVPWDYRAGAKGKMIYIAVAQWMTRLGRCYSP

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_122 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400044937	3 retrocopies	retro_stub_122 , retro_stub_63, retro_stub_64,