RetrogeneDB ID: retro_stub_3

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 8:56848992..56849598(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400046345
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG402015759
• Aliases: None
• Description: None

Sequence

>retro_stub_3
ATGGTGTCCGGTTCAGGAATCTCCGCAAGGAGGATAGTGGTTGATGCTCGTCACCATATGCTTGGTAGGCTCTCATCAAT
TTTGGCTAAGGAACTGCTTAATGGACAGAGAGTTGTTGTTGTTAGGTGTGAAGAGATTTGTCTTTCTGGTGGACTTGTTC
ATCAGAAAATGAAGTATCTCAGGTTCCTTCGTAAGAGGATGAATACTAAGCCTTCTCATGGACCTATTCACTTCCGTGCT
CCCTCTAAGATCCTCTGGAGGACCATCCGTGGGATGATTCCCCACAAAACTAAGCGTGGAGCAGCTGTTCTTGCCTGCTT
GAAGGTTTACGAGGGTGTTCCACCTCCATATGACAAAATCAAGAGGATGGTCATCCCTGATGCTCTCAAGGTGTTGAAAC
TCCAAGCAGGACATAAATACTGTCTCTTGGGTAAGCTTTCATCAGAGGTTGGATGGAACCATTATGACACTATCAAGGAG
CTTGAGAACAAGAGAAAGGAGAGAACCCAGGTAGCATACGAGAGGAGAAAGCAGTTGGCCAAACTCAGGGTTAAGGCCGA
GAAGGCTGCTGAGGAGACGCTCGGTCCTCAACTTGCTAGTTATTGA

Alignment

ORF - retro_stub_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.98 %
• Parental protein coverage: 96.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSGSGISARRIVVDARHHMLGRLSSILAKELLNGQRVVVVRCEEICLSGGLVRQKMKYLRFLRKRMNTK
          MVSGSGISARRIVVDARHHMLGRLSSILAKELLNGQRVVVVRCEEICLSGGLV.QKMKYLRFLRKRMNTK
Retrocopy MVSGSGISARRIVVDARHHMLGRLSSILAKELLNGQRVVVVRCEEICLSGGLVHQKMKYLRFLRKRMNTK

Parental  PSHGPIHFRAPSKILWRTIRGMIPHKTKRGAAALARLKVYEGVPPPYDKIKRMVIPDALKVLRLQAGHKY
          PSHGPIHFRAPSKILWRTIRGMIPHKTKRGAA.LA.LKVYEGVPPPYDKIKRMVIPDALKVL.LQAGHKY
Retrocopy PSHGPIHFRAPSKILWRTIRGMIPHKTKRGAAVLACLKVYEGVPPPYDKIKRMVIPDALKVLKLQAGHKY

Parental  CLLGKLSSEVGWNHYDTIKELENKRKERAQVAYERRKQLAKLRVKAEKAAEEKLGPQLA
          CLLGKLSSEVGWNHYDTIKELENKRKER.QVAYERRKQLAKLRVKAEKAAEE.LGPQLA
Retrocopy CLLGKLSSEVGWNHYDTIKELENKRKERTQVAYERRKQLAKLRVKAEKAAEETLGPQLA

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_3 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG402015759	1 retrocopy	retro_stub_3 ,
Vitis vinifera	VIT_07s0005g06490	1 retrocopy	retro_vvin_22,