RetrogeneDB ID: retro_stub_106

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 3:35205984..35206372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400026015
• Aliases: None
• Description: None

Sequence

>retro_stub_106
AAGCCCAACACTTGAATTGTCATGCCTCACTCTTCCAACAATATCATAGTTACAATGCAACCACAAAAAGAGGAACCACC
AGTGATGCAATGCAAGGATACATTCATGCTTCAAAGTTTTGCTGGCAACCCTAGAACTATTGCAAAGGACATTAATCTCG
AGATATTCAATAAGAAGTCGGAGAAATACGTAAAGGACTGCAAGCTGAAACTGATTTATATATGTTCCACCTCAAGTGCC
ACTGCATGTAAGGGAGGGGTCTTCTTCTCCTAGGGCTATAGTATCCGAATATAGCACTGTAAATATATCCGAGCTTAGTA
ATATTTCAAGGTGATATAATGCACAACAAGACAGCTCGTTTGAGACAAAGGTGAAGGTTTACAGAGTT

Alignment

ORF - retro_stub_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.13 %
• Parental protein coverage: 54.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPNTGIVMPRSTCEVIVTMQAQKEAPPDMQCKDKFLLQSVIVSPGTMAKDITPEMFNKESGNHVEEVKLR
          .PNT.IVMP.S....IVTMQ.QKE.PP.MQCKD.F.LQS....P.T.AKDI..E.FNK.S...V...KL.
Retrocopy KPNT*IVMPHSSNNIIVTMQPQKEEPPVMQCKDTFMLQSFAGNPRTIAKDINLEIFNKKSEKYVKDCKLK

Parental  VAYV-PPQPPPSPVREGSEEGSSPRASISE----NGAEFHNASRTYAEPQDNSSETKALILKL
          ..Y...P...P..VREGS...SSPRA..SE....N..E..N.SR.Y...QD.S.ETK......
Retrocopy LIYI>VPPQVPLHVREGS---SSPRAIVSEYSTVNISELSNISR*YNAQQDSSFETKVKVYRV

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_106 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400026015	3 retrocopies	retro_stub_106 , retro_stub_110, retro_stub_96,