RetrogeneDB ID: retro_stub_63

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 00:24255079..24256038(+)
• 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_63
AAGTTTGCAGAATTGGTCAAGATGGGAGACTTTATAGAGGAGGGTGTTAAATCTGGGAAGATCCAGTCTATGGTCGCATT
GCTAGCTACAAGTAGGGCTTTAAAAACGGGTTCCTTTGGTGGCATAAAAAAGAAAAGGGAGGATGTTTCAGCTGTCACTT
ACCAACAAGGAGGACCGTCCCACCGATACCCTAGTAATCCCTAAATCGTTGTGCATACTTCATACGTCGCATACCCAATA
TATAATAGCCAACCACACTATAATCCACCCCGAGCACCAGCATACCAAAATCCTCCAAGACCATATGTCCCTGTCCAAGC
ACCAATCCACCAGAATAGACCAGCATATGCACCGAGACCACGTCCAAATTTTGAAGCTAGAAATGCTCGAACTTACACAC
CGATTGCCGAACCCTACGCCCAATTGTTTGAAAGGTTGAGGACAGCGGGAGTGCTGCAACCAGTTGAAGGAAAACTTCCT
GATCCAATCCCTCGTAATTTTAATGGAAACAAGCGATGCGCTTACCACTCGGGAATCCAAGGACACGACAGAGAAGATTG
TTATGGGTTAAAGAACCAGATCGAGTCTTTAATCAGAAGAGGAGTAATCAATGCACTCCAGTGCCTCCTAATGTGAATAA
CAACCCTTTGCCAAACCATGAGAATTGGGAAGTCAACATGGTTACTTTTGATGAAGAATATGGGGGCCCTAATTGTCCAG
ACATAGATGAACCAGATGCCATGACATCTTTGGCTCAATATGTTATCACTGTTCAACTAAGGGAACCTCTGACTGTCCAA
ACATATCTCCCAAGAGTTCTAATGACCACTCTAAGTGCTAGAAAGCCTGAATATGACACCAAAGCAATCCCTTGGGACTG
TCGAGCAGACGCCAAGGGCAAGATGATCGACACTGCCGTAGCTCAAGGGATGACTAGGTTGGGGAGGTGTTATGCCCCA

Alignment

ORF - retro_stub_63 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 60.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYAEMEKDTQLKEDASINAQLQVYGRLQTASRAIQAGSIGGIKKKNEDVSAVTYQQGGPSHRYPSNPQIA
          ..AE..K.....E........Q....L...SRA...GS.GGIKKK.EDVSAVTYQQGGPSHRYPSNP.I.
Retrocopy KFAELVKMGDFIEEGVKSGKIQSMVALLATSRALKTGSFGGIKKKREDVSAVTYQQGGPSHRYPSNP*IV

Parental  AHTSYVPYPVYNTQPHYNPPRAPAYQNPPRPYVPVQAQIHQNRPAYAPRPRPNFKARNARTYTPIAESYA
          .HTSYV.YP.YN.QPHYNPPRAPAYQNPPRPYVPVQA.IHQNRPAYAPRPRPNF.ARNARTYTPIAE.YA
Retrocopy VHTSYVAYPIYNSQPHYNPPRAPAYQNPPRPYVPVQAPIHQNRPAYAPRPRPNFEARNARTYTPIAEPYA

Parental  QLFERLRTAGVLQPVQGKLPDPIPRNFDGNKQYAYHSGIQGHDTEDCYGLKNQIESLIKRGVI-KCTPAP
          QLFERLRTAGVLQPV.GKLPDPIPRNF.GNK..AYHSGIQGHD.EDCYGLKNQIESLI.RGVI..CTP.P
Retrocopy QLFERLRTAGVLQPVEGKLPDPIPRNFNGNKRCAYHSGIQGHDREDCYGLKNQIESLIRRGVI<QCTPVP

Parental  PNVNNNPLPNHENRKVNMVTLDEEYRGPDCPDIDEPDAMTSSVQPVITVQLREPLTVQTYLPRVVVTTLI
          PNVNNNPLPNHEN..VNMVT.DEEY.GP.CPDIDEPDAMTS..Q.VITVQLREPLTVQTYLPRV..TTL.
Retrocopy PNVNNNPLPNHENWEVNMVTFDEEYGGPNCPDIDEPDAMTSLAQYVITVQLREPLTVQTYLPRVLMTTLS

Parental  ARKPEYDTKAVPWDYRADAKGKMIDTTLKHQRGTNGFGYEP
          ARKPEYDTKA.PWD.RADAKGKMIDT.........G..Y.P
Retrocopy ARKPEYDTKAIPWDCRADAKGKMIDTAVAQGMTRLGRCYAP

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_63 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,