RetrogeneDB ID: retro_stub_52

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:36586190..36586985(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400020916
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400010119
• Aliases: None
• Description: None

Sequence

>retro_stub_52
ATGGTTGCACCAACTAGAGGTCGTGGTGGTGGTGGATTCATGGGCGGTAGAGGGGATTGTGGAGGAAGAGGAGGAAGAGG
TGGAAAAGGTGGTTTCAGTGGTGGAAGAGGGGGTTTTCGAAGTGGAGGAAATGTGATGAAGCGAGGAGGTGGAAGAGGTG
GAGGAAGGGGACGTGGAGGAATGAAGGGTGGTAGTAAGGTTGTGGTGGAGCCTCATAGACATGGAGGCATGTTCACTGCT
AAGTGTAAGGACGATGCTCTTTGTACTAAGAATTTGGTACCTGGTGAAGCTGTCTACAACGAAAAAAGAATCTTTGTTCA
GAATGAAGATGGAACAAAGGTTGAATACAGACTGTGGAATCCTTTCCGTTCTAATTTAGTACCTGCATTTCTTGGAGGAG
TTTATGACATATGGATTAAACCAGGTGCTCGTGTCCTTTTCCTGGTTGCTGCTTCCGGAAAAAAAGTATCTCATGTCTCA
GACATTGTTGGTCCTGATGGGGTTGTATATGCTGTTAAATTTTCTCACAGAAGTGGAAGGGACTTGGTTTACATGGCTAA
GAAATGTACTAATGTTATTCCCATTATCGAGGATGCTAAACACCCATCGAAATACAAAATGTTGGTTGGAATGGTGGATC
TGATATTTTCTGATGTTGCTCAGCCTGATCAGGCAAGAATTTTAGTTCTGAATGCATCATACTTCTTGAATGTTGGGGGT
CACTTTGTTATCTCAATCAAGGCAAACTGTATTGTTCAACAATGCCAGCGGAAGTCATATTTTCTAAGGAAGTGA

Alignment

ORF - retro_stub_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 82.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGRGDGGGRGGRGGRGGFSGGRGGFGSGGSGMKRGGGRGGRGDRGGRGGGRGRGGMKGGSRVVVEPHRH
          RGG.G..GGRG..GGRGG..GG.GGF..G..G...GG....RG..GGRGGGRGRGGMKGGS.VVVEPHRH
Retrocopy RGGGGFMGGRGDCGGRGG-RGGKGGFSGGRGGFRSGGNVMKRG--GGRGGGRGRGGMKGGSKVVVEPHRH

Parental  GGVFIAKGKEDALCTKNLVPGEAVYNEKRISVQNEDGTKVEYRVWNPFRSKLAAAILGGVDDIWIKPGAR
          GG.F.AK.K.DALCTKNLVPGEAVYNEKRI.VQNEDGTKVEYR.WNPFRS.L..A.LGGV.DIWIKPGAR
Retrocopy GGMFTAKCKDDALCTKNLVPGEAVYNEKRIFVQNEDGTKVEYRLWNPFRSNLVPAFLGGVYDIWIKPGAR

Parental  VLYLGAASGTTVSHVSDLVGPDGVVYAVEFSHRSGRDLVNMAKKRTNVIPIIEDARHPAKYRMLVGMVDV
          VL.L.AASG..VSHVSD.VGPDGVVYAV.FSHRSGRDLV.MAKK.TNVIPIIEDA.HP.KY.MLVGMVD.
Retrocopy VLFLVAASGKKVSHVSDIVGPDGVVYAVKFSHRSGRDLVYMAKKCTNVIPIIEDAKHPSKYKMLVGMVDL

Parental  IFSDVAQPDQARILALNASYFLKAGGHFVISIKANCIDSTVPAEAVFAQE
          IFSDVAQPDQARIL.LNASYFL..GGHFVISIKANCI.........F...
Retrocopy IFSDVAQPDQARILVLNASYFLNVGGHFVISIKANCIVQQCQRKSYFLRK

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_52 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	PGSC0003DMG400010119	1 retrocopy	retro_stub_52 ,