RetrogeneDB ID: retro_stub_94

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 11:35222182..35223381(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400028548
• Aliases: None
• Description: None

Sequence

>retro_stub_94
ATGGCTTCCGGGGGAAAGGGAATGTTGGAGAAGGTGAAGAGGTTTTTGAAGATTATATATTTCATGGTGGCGATGTTGGC
ATTGTTGCTGGTACTATCGGCGCCGCTGATTGTGGCAATTGGGGATGGTTTGGTACCAAGTGTGTTGATTTCGACCTTTA
CATGCGTAAGATGTTACAGTTTCAAAGAACATTTGCAGAGATATGCCTTCAAAAGCACATTGACGGACATTCCTCTCGTT
TCTGTGATGAGATCTCTTATTATCCCCTATGTTTATTCTTTGTGTGATGGCCCTGCTCTTTCGCATGGACCATACCTCGG
AATGGTTATATTCTGTTCTATCATTTCCATTATTCTTCTTTCTATCAAAGCTTGTATTTTCTGTCAATTCATATCTGGAG
GTTGAAGCTTCATCTTCTATCTCAAGGCAAAGGCCTCATCTGAAAAAGTCATGGGGGTGTGCCTGTGTTGTTTCTTTCTT
CGGTAGTCTTAGCTCTTGGACATGCTATAATTGCTTACAGAACAATCTTTTGAGCAAGGAGGAAGCTTTTGTTTCACCGA
GTTGACCCAGAAGCTGTCCTTTCGTGCAAAGTTGGATTCTCTTCATACAGTAAGGTACCACAATCACCAATTCCGACAGG
TAAAACAAGAACTGAGAGTGATATGAGGAGAAAACTTGCAGGATCGGCTCATGAGGATGGGAAAGTCCCTGCTATATTGC
TTGCTGATGTTGACAGTTCTTTCATTTCTTGCCTTGGGCTCTCTCTTCATTACAAACTTTGCTTGCCTGGCTCACCTTAC
TGTTCTTTGTCTTTCAGACCTTCTTCTGCTCACCCATTGCAGGTTTTGTCAAAAAGTGATTATCGTATTCGGAGGTGCCA
CAGTAGTCAATTTCATACCCACACTCTCTCTATGCCTCTTTTAGATGTGTCTCCAACTTCCCCAGTTCTGTCTGAAGAAA
TTCCTAGTTTCAGCCTAGATGAAACTGGTGATGATGATGATGTTGGTAAGGTGGGATGTTCATTCCCAGTATGAGATGTT
GAAGGGAATAATCAGTTTATTACTGTTCTAGTGCATGGTTTTGGAGCCGGAGGTTTCTCTTAGAGAATGATGATGGATGA
ACTAGCCCGATAGGTAGGTTGTGCAGTCACAGCCCTCTACAGGCCAGGATGGGGATTGACATCTAGGCCATGTCAGAGA

Alignment

ORF - retro_stub_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 63.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGSGGKGMLEKVKRFLKIIYFMVAMLASLLVLSAPLIVAIGDVLVPSVLISSFTCVKCYSFKEHLHRYAF
          M.SGGKGMLEKVKRFLKIIYFMVAMLA.LLVLSAPLIVAIGD.LVPSVLIS.FTCV.CYSFKEHL.RYAF
Retrocopy MASGGKGMLEKVKRFLKIIYFMVAMLALLLVLSAPLIVAIGDGLVPSVLISTFTCVRCYSFKEHLQRYAF

Parental  KSSLTDIPIVSIMRSLIITCVYSLCDGPALSHGPYLGTVTFCSIISVILLS-IKACVFSVNSYLEVEASS
          KS.LTDIP.VS.MRSLII..VYSLCDGPALSHGPYLG.V.FCSIIS.I.L......VFSVNSYLEVEASS
Retrocopy KSTLTDIPLVSVMRSLIIPYVYSLCDGPALSHGPYLGMVIFCSIIS-IILL>LSKLVFSVNSYLEVEASS

Parental  SISRQRLHLKKSWG-MPVLFLSSVVFALGHTVIAYRTSCRARRKLLFHRVDPEAVLPCKVVFSAYNKVPR
          SISRQR.HLKKSWG..PVLFLSSVV.ALGH..IAYRT...ARRKLLFHRVDPEAVL.CKV.FS.Y.KVP.
Retrocopy SISRQRPHLKKSWG>VPVLFLSSVVLALGHAIIAYRTIF*ARRKLLFHRVDPEAVLSCKVGFSSYSKVPQ

Parental  SPTPTGKTRTESDMRRKLAGSAHEEGEVPAILLADVDSSFISCLGLSVHYKLCLPGSPYRSLSSTPSSAN
          SP.PTGKTRTESDMRRKLAGSAHE.G.VPAILLADVDSSFISCLGLS.HYKLCLPGSPY.SLS..PSSA.
Retrocopy SPIPTGKTRTESDMRRKLAGSAHEDGKVPAILLADVDSSFISCLGLSLHYKLCLPGSPYCSLSFRPSSAH

Parental  PLHVLSKSDYRIRRSQSTQFHTHTLSMPLLDVSPTSPVLSEEIPTFCLDETGDEDDVGKVGCSFPVRDVE
          PL.VLSKSDYRIRR..S.QFHTHTLSMPLLDVSPTSPVLSEEIP.F.LDETGD.DDVGKVGCSFPV.DVE
Retrocopy PLQVLSKSDYRIRRCHSSQFHTHTLSMPLLDVSPTSPVLSEEIPSFSLDETGDDDDVGKVGCSFPV*DVE

Parental  GNNQFGIVLVHGFGGGVFSWRNVMDDLAQQVGCAVTAFDRPGWGLTSRPRQR
          GNNQF..VLVHGFG.G.FS.R..MD.LA..VGCAVTA..RPGWGLTSRP.QR
Retrocopy GNNQFITVLVHGFGAGGFS*RMMMDELAR*VGCAVTALYRPGWGLTSRPCQR

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_94 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	PGSC0003DMG400028548	1 retrocopy	retro_stub_94 ,