RetrogeneDB ID: retro_stub_61

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:49017046..49018054(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400018386
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400014503
• Aliases: None
• Description: None

Sequence

>retro_stub_61
ATGGCGTCTTCTGGAGCTTGGACTTATCGAGATCGAACTTCCGAGTTCACGTCTTTGTCCAAAACATTGAAGAAGATCGC
AGGAAGTACCGGATCAGATCATGAATCACAACAGAATTTTGCTTCTTCTACCACAAAATTACTACCAATTCCAGATCGAT
CTGAATTCAACAAGAAGGCATCGAGAATTGGGTTGACGATCCATCAAACCTTTCAGAAAATCGATAGGCTTGCTAAATTG
GCAAAACGATCATCGATTTTTGACGATCCAAGCAAGGAAATTCAGGAATTGACAACTTTCATAAAGAATGATATCACATC
ACTCAATGTCGGTGTTTCTGATTTACAAGCCCTTCAAGACATGGATGTAGCTGATGGAACTCATTCAAAAGATACAATTG
TTCATTGTACTGCGATTTGTGATGATCTGAAGACGAGACTTATGGCAGCTACAAAATCATTCCAGGAGGCACTTACTATA
AGGACAAAGAACATGAAAGCTCACGAAGATCGAAAACAAATATTTTCTACAAATCTCTCTAGAGAAAATCCTTTGAAACA
ACCTCCAAAGACCTTAGCAGAGCCACCTCCATGGTCAATTCCTACATCAGGAAGTGGTGGAAATGATGTTCAGGGCAGCA
ATCAATTAAGACGGAGATTGGCTTCAGACAATCCTCCATCTAACGAAATGGAAATGTCCATGTTACAAGATCAGGTTCCG
AGACAAGAAAGTTACTCTCAGAGTAGGGCAACTGCTCTTCAAAATGTTGAATCAACTATTTCAGAATTGGGCGGAATATT
CACACATCTAGCTACGATGGTTGCACAACAAGGTGAGCTTGCTATAAGAATTGACGATAACATAGATGAGTCATTAACAA
ATGTTGAAGGTGCACAAGGTGCTTTGTTAAAGTACTTAAATCGAATATCATCAAACAGGTCTCTCATGATCAAAATTTTT
CTTGTTGTTATACTTTTTCTCTGTGTATTTATATTTTTTCTTGCGTGA

Alignment

ORF - retro_stub_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.2 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDRTQEFQSIAERLKKSFSSVQNGPISSSTSSGSRSEEQRTTIAMQSEFNRRASKIGFGIHQTSQKLAKL
          RDRT.EF.S....LKK...S...G....S......S......I...SEFN..AS.IG..IHQT.QK...L
Retrocopy RDRTSEFTSLSKTLKKIAGST--GSDHESQQNFASSTTKLLPIPDRSEFNKKASRIGLTIHQTFQKIDRL

Parental  AKLAKRTSVFDDPTTEIQELTAVIKQDITALNSAVVDLQLHSNARNESG--NSDTTSHSTTVVDDLKNRL
          AKLAKR.S.FDDP..EIQELT..IK.DIT.LN..V.DLQ.........G....DT..H.T...DDLK.RL
Retrocopy AKLAKRSSIFDDPSKEIQELTTFIKNDITSLNVGVSDLQALQDMDVADGTHSKDTIVHCTAICDDLKTRL

Parental  MTATKEFKEVLTMRTENMKVHENRRQMFSSSTTKEASNPFMRQRPLASRNTASTSASPPPWANDSPSSSQ
          M.ATK.F.E.LT.RT.NMK.HE.R.Q.FS..T.....NP.......................ND...S.Q
Retrocopy MAATKSFQEALTIRTKNMKAHEDRKQIFS--TNLSRENPLKQPPKTLAEPPPWSIPTSGSGGNDVQGSNQ

Parental  LFPRKQGDGNTQPLLQDQQQQQQQIVPLQDSYMQSRAEAFQNAESTIHELGSIFNQLATLVSEQGEVAIR
          L..R...D....P.........Q..VP.Q.SY.QSRA.A.QN.ESTI.ELG.IF..LAT.V..QGE.AIR
Retrocopy LRRRLASDN--PPSNEMEMSMLQDQVPRQESYSQSRATALQNVESTISELGGIFTHLATMVAQQGELAIR

Parental  IDENMDDTLTNVEGAQGALLKYLNSISSNRWLMIKIFFVLIFFLMIFLFFVA
          ID.N.D..LTNVEGAQGALLKYLN.ISSNR.LMIKIF.V.I.FL..F.FF.A
Retrocopy IDDNIDESLTNVEGAQGALLKYLNRISSNRSLMIKIFLVVILFLCVFIFFLA

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_61 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	PGSC0003DMG400014503	1 retrocopy	retro_stub_61 ,