RetrogeneDB ID: retro_stub_64

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 00:30831169..30832127(+)
• 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_64
GAAGTTTGCAGAATTGATCAAGATGGGAAACTTCATAGAGGGGGTGTTAAATCTGGGAAGATTCAGTCTATAGTCGTATT
GCAAGCTGCAAGTAGGCCATGTAATCGGGTTCCATTAACAGCATCAAGAAGAAGAGGGAGGATGTTTCAACTATCACTTA
CTAACAAGGAGGACAATCCCATCGATACCCAAACAATCCCCAAATTGTTGCACATACTTCTTACATCCCATACCCAGTAT
ATAATACCCAACCACACTATAATCCACCCCGAGCACTATCATACCAAAATCCACCAGACCATATCTCACTGTCAAAGTAC
CAATCCACCAAAATAAACCAACATATGCATCGAGACCACGTCCAAATCTCGAAGCAAGAAATGCTCGCGCTTACACACTA
TTTGTCGAGCCCTATGCCTAATTGTTTGAGAGGTTGAGGACAGTAGGAGTGCTGCAACCAGTTGAAGGGAAACTTCCCGA
TCCAATCCCTCGTAACTTCGATAGAAACAAGCGATGCGCTTACCACTCGGGAGTCCAAGGACACAACACAAAAGATTGTT
ATGGTTTGAAGAACCAGATCGAGTCTTTGATCAGGAGAGGAGTAATCAAATACACTCCAACACCTCCCAATGTAAACAAT
AACCCCTTGCCAAACCATGAGAATCGGAAGGTCAACATGGTTACTCCAGATGAAGAATATGAGGGCCCTAACTGTCCAGG
CATAGATGAAGCAAATGCCATGACATCTGCGGCGCAACCTGTTATCATTGTTCAACTAAGGGAACCTCTGACTTTACAAA
CATATCTCCCAAGAGTTGTAGTGACCACCCTAATCACTAGAAAGCCTGAGTATGACACAAAAGCAGTCCCATGGGACTAT
CGAACAGGCGCCAAGGTCAAGACGATTGATACTGCCGTGGCTCAGGGAATGAATTGGTCAGGAATGTTTTATGCCCCG

Alignment

ORF - retro_stub_64 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 60.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QYAEMEKDTQLKEDASINAQLQ-VYGRLQTASRAIQAGSIGGIKKKNEDVSAVTYQQGGPSHRYPSNPQI
          .......D..L..........Q.VY.R......A...GSI..IKKK.EDVS..TY.QGG.SHRYP.NPQI
Retrocopy EVCRIDQDGKLHRGGVKSGKIQ<VYSRIASCK*AM*SGSINSIKKKREDVSTITY*QGGQSHRYPNNPQI

Parental  AAHTSYVPYPVYNTQPHYNPPRAPAYQNPP-RPYVPVQAQIHQNRPAYAPRPRPNFKARNARTYTPIAES
          .AHTSY.PYPVYNTQPHYNPPRA..YQNPP.RPY..V...IHQN.P.YA.RPRPN..ARNAR.YT...E.
Retrocopy VAHTSYIPYPVYNTQPHYNPPRALSYQNPP<RPYLTVKVPIHQNKPTYASRPRPNLEARNARAYTLFVEP

Parental  YAQLFERLRTAGVLQPVQGKLPDPIPRNFDGNKQYAYHSGIQGHDTEDCYGLKNQIESLIKRGVIKCTPA
          YA.LFERLRT.GVLQPV.GKLPDPIPRNFD.NK..AYHSG.QGH.T.DCYGLKNQIESLI.RGVIK.TP.
Retrocopy YA*LFERLRTVGVLQPVEGKLPDPIPRNFDRNKRCAYHSGVQGHNTKDCYGLKNQIESLIRRGVIKYTPT

Parental  PPNVNNNPLPNHENRKVNMVTLDEEYRGPDCPDIDEPDAMTSSVQPVITVQLREPLTVQTYLPRVVVTTL
          PPNVNNNPLPNHENRKVNMVT.DEEY.GP.CP.IDE..AMTS..QPVI.VQLREPLT.QTYLPRVVVTTL
Retrocopy PPNVNNNPLPNHENRKVNMVTPDEEYEGPNCPGIDEANAMTSAAQPVIIVQLREPLTLQTYLPRVVVTTL

Parental  IARKPEYDTKAVPWDYRADAKGKMIDTTLKHQRGTNGFGYEP
          I.RKPEYDTKAVPWDYR..AK.K.IDT.........G..Y.P
Retrocopy ITRKPEYDTKAVPWDYRTGAKVKTIDTAVAQGMNWSGMFYAP

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_64 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 ,