RetrogeneDB ID: retro_stub_20

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 11:37281334..37282849(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400032529
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400007545
• Aliases: None
• Description: None

Sequence

>retro_stub_20
ATGGCCTCCTTTCAATTATCTCTCACCAATCCCAAACACAAAAGAAACCATACTTCCCTAGAAGTTTTTCCATTATGGAA
CACATTCAAATCCAAGAACCTCTCTTTCCCAAACAAAAGACTTTCACCAAACCTATCTTTGAAAATATCTTCATGTCTTT
CAAATTTAGAGGACAACAATATTGAACTCCAACAATATGATCAAGAAGAGAAAAAACCCCTTCATGAGATGTGGAGAGAA
ATTCAAGGATGTAACAATTGGAAAGGTTTACTTGATCCTATGGATTCTCATCTAAGAAAAGAAATCATTCGTTATGGTGA
ATTTGCTCAATCTTGTTATGACTCATTTGACTATGATCCTCATTCAAAATATTGTGGTACTTGCAAGTATCAACCATCAC
ACTTCTTTGACAAGATCAACATGTTGAAAAAAGGTTATGAAATGAAAAGATACTTATATGCAACTTCAAATATCAACTTA
CCAAATTTCTTCCAAAAATCGAAAATGAGCAATGTATGGAGCCAACACGCGAACTGGATGGGGTATGTAGCCGTAGCCAC
AGATCCTGAAGAAATTAAACGTCTAGGGAGACGTGACATAGTGGTTGCATGGCGTGGCACGGTGACTTACCTAGAATGGA
TCCATGACCTACAAGACATTTTACATCCTGCTCATTTTCGCGATGATCCTAACATCAAGATTGAGTCAGGGTTCTTCGAT
ATGTATACTAAAAAAGAAAATAATTGTCACTATGCTTCATTTTCAGCTCGTGAACAAATTTTAGCGGAGATTAATAGATT
AATCGAAAAATACCAAGGTGAAGAGCTAAGTATTACTATTACAGGACATAGTCTTGGTGCAGCATTGGCTTTGTTAAGTG
CTTATGACATAGCTGAGATGAAATTGAATATTTTACATGATGGTAAGTCTATTACAAAAATTATTCCTGTTACTGTTTTT
TCATTTGCTGGACCTAGGGTTGGAAATCTTAAATTTAAAGAAAGATGTGAAGAGCTTGGAATTAAAGTTTTAAGAGTTAT
AAATGTGCATGACAAAGTGCCAACAGTGCCTGGAATTATTACAAATGAGAAATTTCTATTCCAAAAACAATTGGAAGAGA
AATTTTCATTTGCTTGGAGTTATGCTCATGTAGGGGCGGAGCTAGCCTTAGATCATCATCGTTCTCCATTTCTAAAGCCC
AATAGTGATTTGGGCTCTGCACATAACCTTGAGGCCCATTTACATCTTGTTGATGGGTACCATGGGAAGGTACGCGCTTT
TCGCTCTGCCACGGGTAGGGATGTTGCCCTTGTGAATAAGGATTCGAGTTTCTTGAAGGAGGAGTATGGCGTGCCACCGT
TTTGGTGGCAAGATGAGAATAAAGGTATGGTGAGAACGAGCGATGGGCAATGGGTGTTGCCGGAGAGGCCTGTAATTGAG
GCCCATCCACCCGATACGGCTCATCATTTTCAACAAGTCCTTAAACTTGCGAGAGCTAGGTTAAATTTACCATAA

Alignment

ORF - retro_stub_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.96 %
• Parental protein coverage: 56.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRWLEIHGQDDWVGMLDPMDPILRNELIRYGEMAQACYDAFDFDPYSKYCGSCKFPRRKFFDGLGMAEYG
          ..W.EI.G...W.G.LDPMD..LR.E.IRYGE.AQ.CYD.FD.DP.SKYCG.CK.....FFD...M...G
Retrocopy EMWREIQGCNNWKGLLDPMDSHLRKEIIRYGEFAQSCYDSFDYDPHSKYCGTCKYQPSHFFDKINMLKKG

Parental  YDITRYLYATSNINLPNFFKQSRWPKIWSKNANWIGYVAVSND-ETTKRLGRRDITIAWRGTVTRLEWIA
          Y...RYLYATSNINLPNFF..S.....WS..ANW.GYVAV..D.E..KRLGRRDI..AWRGTVT.LEWI.
Retrocopy YEMKRYLYATSNINLPNFFQKSKMSNVWSQHANWMGYVAVATDPEEIKRLGRRDIVVAWRGTVTYLEWIH

Parental  DLMDYLRPISSDNIPCPDPNVKVESGFLDLYTDKDEKCRYCKFSAREQILTEVKRLIEMYPDEEMSITVT
          DL.D.L.P......P....N.K.ESGF.D.YT.K...C.Y..FSAREQIL.E..RLIE.Y..EE.SIT.T
Retrocopy DLQDILHPAHFRDDP----NIKIESGFFDMYTKKENNCHYASFSAREQILAEINRLIEKYQGEELSITIT

Parental  GHSLGSALAILSAYDIVETGLNV----KADTSAVPICVFSFSGPRVGNVRFKERIEKLGVKVLRVVNVHD
          GHSLG.ALA.LSAYDI.E..LN.....K..T...P..VFSF.GPRVGN..FKER.E.LG.KVLRV.NVHD
Retrocopy GHSLGAALALLSAYDIAEMKLNILHDGKSITKIIPVTVFSFAGPRVGNLKFKERCEELGIKVLRVINVHD

Parental  IVPKSPGLVLNE
          .VP..PG...NE
Retrocopy KVPTVPGIITNE

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_20 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400007545	1 retrocopy	retro_stub_20 ,
Solanum lycopersicum	Solyc09g065890.2	1 retrocopy	retro_slyc_39,