RetrogeneDB ID: retro_stub_5

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:46508951..46509821(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG401028714
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400012286
• Aliases: None
• Description: None

Sequence

>retro_stub_5
ATGGCTGATGCATTTGAAGAGGATGCTGAGAATACTGTTTCAATTGGAGAGTTTCTCGAAGAACAGGAACTGGAGGAAGA
TTTGGTCTTAGGTGGTGATGAAGGCAAGGAGTGCACCTATAGTAAAGGTTATATAAAGAGACATGCTATTTTTTCTTGTT
TGACATGCACACCAGATGGGAATGTTGGAGTATGCACAGCTTGTAGCCTCTCTTGCCATGATGCTCATGAGATTTTGGAA
CTTTGGACGAAGAGAAACTTCAGGTGTGACTATGGAAATTCAAAGTTCGGGGAGTTCTTCTGCAAGCTTGATGCTAGCAA
AGATGTTGAAAGCACGAAGAATACATATAATCACAATTTCAAAGGTTCATACTACACATGTGGCCGGCCATATCCTGATC
ATGATGTTGAAGACCAATTGGAGAATCTCCAATGCTGCATCTGTGAGGACTGGTTTCATGAGGAGCATATTGGTCTTGAG
TCCTCTGATATGGTTCCAAGGGATGCCAAAGGGGAGCCTCAATTTGAGGATTTTATCTGCCAGGGGTGCGCAACTGTTTG
TTCTTTTTTAAAGCTATATCCTGATTCTATCTTTGCACCAGTCCAGCAGCAGACTACTACAAATTCCTCAAGGGACAAGG
AGGTGGTTGAAGATGCACCCTTGACTGTGGGATCTTCTAAGGAACTTAGCAATGAAAGTTCCTCAGTTGAGACTCCTATA
ACCGATAATAATCCTAAAGAAGACTGCAACAGAAAGGTTCTTCTTCTTGGAGAAAATGCCACAACAAACACACTCCTTAA
TCAGCGTAACACAGTTATTGGTCCTAATACCAAATTGCTGGTCCTAGTACCAAATGTGTTGTTGGACTGA

Alignment

ORF - retro_stub_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 68.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADAFEEDGENTVSIGEFLQDLEEQELEADLVLGGDEGKECTYSKGYMKRQAIFSCLTCTPNGNAGVCTA
          MADAFEED.ENTVSIGEF...LEEQELE.DLVLGGDEGKECTYSKGY.KR.AIFSCLTCTP.GN.GVCTA
Retrocopy MADAFEEDAENTVSIGEF---LEEQELEEDLVLGGDEGKECTYSKGYIKRHAIFSCLTCTPDGNVGVCTA

Parental  CSLSCHDGHEILELWTKRNFRCDCGNSKFGEFFCKLDASKDVENTKNSYNHNFKGSYCTCGRPYPDPDVE
          CSLSCHD.HEILELWTKRNFRCD.GNSKFGEFFCKLDASKDVE.TKN.YNHNFKGSY.TCGRPYPD.DVE
Retrocopy CSLSCHDAHEILELWTKRNFRCDYGNSKFGEFFCKLDASKDVESTKNTYNHNFKGSYYTCGRPYPDHDVE

Parental  DQLENLQCCICEDWFHEEHLGLESSDMVPRDDKGEPQFEDLICQGCATVCSFLKLYPDSIFAPVQQQTTT
          DQLENLQCCICEDWFHEEH.GLESSDMVPRD.KGEPQFED.ICQGCATVCSFLKLYPDSIFAPVQQQTTT
Retrocopy DQLENLQCCICEDWFHEEHIGLESSDMVPRDAKGEPQFEDFICQGCATVCSFLKLYPDSIFAPVQQQTTT

Parental  NASKDKEVVEEAPLTVGSSKELSNGSSSVETPVTDNSPKEDCNGKA-VLGENAATNTLLNQCNTVAGPST
          N.S.DKEVVE.APLTVGSSKELSN.SSSVETP.TDN.PKEDCN.K...LGENA.TNTLLNQ.NTV.GP.T
Retrocopy NSSRDKEVVEDAPLTVGSSKELSNESSSVETPITDNNPKEDCNRKVLLLGENATTNTLLNQRNTVIGPNT

Parental  KCVV
          K..V
Retrocopy KLLV

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_5 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400012286	1 retrocopy	retro_stub_5 ,