RetrogeneDB ID: retro_stub_78

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:54190699..54191459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400007914
• Aliases: None
• Description: None

Sequence

>retro_stub_78
GAGCATTTTCAGTTCGTAGTCGAAGATCCATTGACACAACACTTGGTGGTAAAAATCTATGACGATGAAGGGCTTCAGTC
AGCTGAACTAATTGGATGTTCCCATATCTGTTTGAATGAGCTTGAGCCTGGTAAAGCGAAGGATATCTGGTTGAAGTTGG
TGAAAGATTTGGAAATTCAGAGAGATAAGAAAAATAGGGTCCAGGTGCACTTGGAGCTATTGTACTGCCCGAAATGGCAT
GAACAATGGGCTAAGTAAGCTTTTTTCTCAGAATGAGTCAATGACTTCATTAGAGAGGGTTCTTAAAAACTCGGCAGAAG
GAAAAGAAGTTAGTCCAAACGGAAGTGAAATCAACAATAGAAGAGAGGTAATAGTACGAGGGGTACTTTCTGTTTCCGTG
GTATCAGGTAATGACCTGCCCCCAGCTGATATAGGGGGGAAGGCTGACCCCTAAGTCGTTCTGATCATGAAGAAGGCTCA
AATCAAGAGTAAAACCAGGGTTGTAAATGAAAGTCTAAACCCGATATGGAATCAAACTTTTGACTTTGTTCTTGAGGACG
GATTACATGACATGTTAATGCTGGAAGTCTGGGACCATGACAAATTTGGAAAGGATTTCATGGGAAAATGCATACTGACT
TTAAAAAGGGTTCTAATTGAAGGTGAATACAAAGACTCGTACGAATTAGCTGAGGTTAAATCAGGGAAACTGAACTTGCA
TCTCAAATGGAATCCACAACCAATATACAGAGACTACCAG

Alignment

ORF - retro_stub_78 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.34 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EHFEFVVEDPLTQHLVVKIYDDEGLQSAELIGCAHICLNELEPGKVKDIWLKLVKDLEIQRDQKNRGQVH
          EHF.FVVEDPLTQHLVVKIYDDEGLQSAELIGC.HICLNELEPGK.KDIWLKLVKDLEIQRD.KNR.QVH
Retrocopy EHFQFVVEDPLTQHLVVKIYDDEGLQSAELIGCSHICLNELEPGKAKDIWLKLVKDLEIQRDKKNRVQVH

Parental  LELLYCP-NGMNNGLSNPFSQNESMTSLERVLKNSAEGKEASPNGSEINNRREVIVRGVLSVTVVSADDL
          LELLYCP.NGMNNGLS..FSQNESMTSLERVLKNSAEGKE.SPNGSEINNRREVIVRGVLSV.VVS..DL
Retrocopy LELLYCP>NGMNNGLSKLFSQNESMTSLERVLKNSAEGKEVSPNGSEINNRREVIVRGVLSVSVVSGNDL

Parental  PPADIGGKADPYVVLIMKKAQIKNKTRVVNESLNPVWNQTFDFVVEDGLHDMLMLEVWDHDTFGKDFMGR
          PPADIGGKADP.VVLIMKKAQIK.KTRVVNESLNP.WNQTFDFV.EDGLHDMLMLEVWDHD.FGKDFMG.
Retrocopy PPADIGGKADP*VVLIMKKAQIKSKTRVVNESLNPIWNQTFDFVLEDGLHDMLMLEVWDHDKFGKDFMGK

Parental  CILTLTRVLMEGEYKDTYELAEAKSGKLNLHLKWNPQPIYRDYQ
          CILTL.RVL.EGEYKD.YELAE.KSGKLNLHLKWNPQPIYRDYQ
Retrocopy CILTLKRVLIEGEYKDSYELAEVKSGKLNLHLKWNPQPIYRDYQ

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_78 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400007914	2 retrocopies	retro_stub_129, retro_stub_78 ,
Solanum tuberosum	PGSC0003DMG401030679	1 retrocopy	retro_stub_69,