RetrogeneDB ID: retro_stub_45

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:71887332..71888703(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400000023
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400004771
• Aliases: None
• Description: None

Sequence

>retro_stub_45
ATGGCTACTCTTGCTGCTTCTTTCTTAGCAGATCTGGACGAATTGTCCGATAACGAAGAGACTCCATTATGGATAGAGGA
ACATGATGGAGAATTGGATGATATTTTCAAACTGCAAAATTCATATTGCTACATTGACGTTATGCACAGAGTTGAAGATG
CCTTAAGTTGTGATCGTAAGCCTATATTAGGTGATTCAGAATATGATGCTTTGATAATGGACTGTAATGCATTATCAATC
GATATTGAGAATGAAATTTTTATAATCCACAATTTTATACGCGACAAGTACCGATTGAAATTTCCTGAATTGGAGTCACT
TGTTAATCACCCAATTGATTATGCTCGGGTTGTTAAAAAGATTGGGAATGCAATGGACATGACTTTAGTTGATTTGGAAG
GATTATTACCCTCAGCTGTTATCATGGTTGTCTCTGTTACCGCGTCTACTACCAGTGGCAAGCCATTGCCACAAGACGTT
TTACACAAGACGTTGGAAGCATGTGACAGAGCTCTTTCTATTGATTCAGCAAAGAAAAAAGTAGTTGATTTTGTTGAGAG
TCGAATGGGATTTATCGCTCCCAATCTTTCTGCTGTAGTTGGGTGTGCAGTTGCTGCTAAACTTATAGCTACTGCTGGTG
GTCTCTCGTCCTTGGCAAACATCCCCGCTGATTGCATCAAGCTTCTTGGTGCCAAAAGGAATATTAATAATTTAGCAGGG
TTCTCAACAGCCAAGTCTCATCACATAGGAGGTTGTTATATTGAGGAAACTGATATAATTCAGAGTACACCTCCTTCCTT
AAGGAAGCAAGCCTATGGACTGTTGGCAGATAAATCTATATTAGCAGCCCGTATGGACTCAGCCAGAGGAGATCCGACTG
GGCAATATGGAACATCTCTTAAGGGTATTATTCTTAAGAAGATGGAGAAATTGCAAGAGTTACCTCCAGCAAAGCAACCA
AAGCCTCTTCCAGTTCCATTAGATTCTAATGCTTATAAGAAAAAGAGAGGCGGTAGTCGGAAGAGAAAGATGAATAAGAG
ATATGAGATTACGGAGAGGCAGAAGCTAGTAAATAGGATCAAGTTTGGAGTAGCTGAAGAGAGCTCCTTGGGGGATGGAT
TAGGGCAGGGCTATGGCATGCTTAGTCAAGCAGATGGAATTGGCAAGTTACGTCTATCAGTTATTAAGAAGAAATTCAAA
AGCAGCAGTACTAGTATTCGTGTATACTCAGGCTTGACTTCAAGTTTGGCCTTTACCCCAGTTCAAGGGATCGAGCTATC
AAATCCTGATCAGGCCAAGCATGCAATTACCAGAAGTCGTAGCACCTATTTCTCTGAAACTGCAACATTCTCCAAGATTA
AGACAACATGA

Alignment

ORF - retro_stub_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 82.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLEDEPEYQLIVDCNALSVDIENEIVIIHNFIRDKYRLKFPELESLVHHPIDYARVVKKIGNEIDLTLVD
          .L.D.....LI.DCNALS.DIENEI.IIHNFIRDKYRLKFPELESLV.HPIDYARVVKKIGN..D.TLVD
Retrocopy ILGDSEYDALIMDCNALSIDIENEIFIIHNFIRDKYRLKFPELESLVNHPIDYARVVKKIGNAMDMTLVD

Parental  LEGLLPSAIIMVVSVTASTTSGKPLPEDVLQKTVEACDRALALDSAKKKVLDFVESRMGYIAPNLSAVVG
          LEGLLPSA.IMVVSVTASTTSGKPLP.DVL.KT.EACDRAL..DSAKKKV.DFVESRMG.IAPNLSAVVG
Retrocopy LEGLLPSAVIMVVSVTASTTSGKPLPQDVLHKTLEACDRALSIDSAKKKVVDFVESRMGFIAPNLSAVVG

Parental  SAVAAKLMGTAGGLSSLAKMPACNVQLLGAKRK--NLAGFSTATSQFHVG--YIEQTELFQSTPPSLRMR
          .AVAAKL..TAGGLSSLA..PA....LLGAKR...NLAGFSTA.S..H.G..YIE.T...QSTPPSLR..
Retrocopy CAVAAKLIATAGGLSSLANIPADCIKLLGAKRNINNLAGFSTAKSH-HIGGCYIEETDIIQSTPPSLRKQ

Parental  ACRLMAAKSTLAARVDSINGDPVGKTGRSLREEIRKKIEKWQEPPPAKQPRPLPVP-DSEP-KKKRGGRR
          A..L.A.KS.LAAR.DS..GDP.G..G.SL...I.KK.EK.QE.PPAKQP.PLPVP.DS...KKKRGG.R
Retrocopy AYGLLADKSILAARMDSARGDPTGQYGTSLKGIILKKMEKLQELPPAKQPKPLPVPLDSNAYKKKRGGSR

Parental  LRKMKERYAITDMRKLANRMQFGIPEESSLGDGLGEGYGMLGQAGSGKLRVSVGQSKLAAKVAKKFKEKS
          .RKM..RY.IT...KL.NR..FG..EESS....LG.G.G.....G.G.L....G..KL...V.KK....S
Retrocopy KRKMNKRYEITERQKLVNRIKFGVAEESS----LGDGLGQ----GYGMLSQADGIGKLRLSVIKKKFKSS

Parental  YGSSGATSGLTSSLAFTPVQGIELSNPQALANQLGSGTQSTYFSDTGTFSKIKRT
          ..S....SGLTSSLAFTPVQGIELSNP............STYFS.T.TFSKIK.T
Retrocopy STSIRVYSGLTSSLAFTPVQGIELSNPDQAKHAI-TRSRSTYFSETATFSKIKTT

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_45 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G60170	1 retrocopy	retro_atha_27,
Brassica oleracea	Bo1g091740	1 retrocopy	retro_bole_6,
Brassica rapa	Bra031522	1 retrocopy	retro_brap_23,
Solanum tuberosum	PGSC0003DMG400004771	1 retrocopy	retro_stub_45 ,