RetrogeneDB ID: retro_stub_1

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:41319974..41321435(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400034632
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400015327
• Aliases: None
• Description: None

Sequence

>retro_stub_1
ATGGAGTCAGTAAACAAGAAAACAGAGTTGGTTTTCATTCCTGTTCCTGGTATGGGCCACCTAGTACCCACACTTGAGAT
GGCAAAGGTTCTAATAGCTAGAGATGAACATCTCGTCATTACAGTCCTCGTAATCAAGCTGCCTTCTGACAACATGCTCA
GCTCCTATATTGAATCAGTCTCGACAAATCCAAACTACAACTCTCAAATGAAGTTCATTGAACTCCCTCAATATGAGTCC
ATCTTACAGTCAATCACAAACACAACTTTCATCACATTTTTATCCAGTCAAAAGCCTCAAGTCAGAAATTCTGTGATTGA
AATCTTGAATTCAGGATCAAATCGTCTTGCGGGCCTTGTTATTGACATGATGTGTACAGCAATGATAGACGTGGCCAATG
AATTTGGCCTCCCGACTTATGTTTTCTACACGTCTGGTGCTGCCATGCTTGGTCTTCAGCTTCATTTGCAGACTCTCAGG
GATGATTTTAACCAAGACGTGACAGAATACAAGGATGATCCAGAAGCAGAGCTTTCGGTGACAACGTATGGAAACCCATT
TCCAGCTAAATGTTTGCCATCTATAGCCTTTGACAAGGATGGTGGTTCCACAATGTACCTTGATCTTTCTAAAAGGCTTC
GAGAAGCTAAAGCTATCCTAGTCAACACTTTCTCCGAATTCGAATCTCATGCTGTCAAATCCCTCTCCCTCGATGAGAAA
ATCCCACTTGTATACCCAGTCGGACCTTTGCTAAACCTTGATAACGATCACGGTAACAATCAAGATTCTTCTCAACATCA
AACTATAATCAACTGGTTAGATGATCAACCCGATTCATCAGTAGTGTACCTCTGCTTTGGAAGCTTAGGAAGTTTCAACG
AGGAGCAAATAAAGGAAATTGCATATGCTTTGGAGAAGAGCGGATGTCGATTCTTGTGGTCCCTAAAGAAGCCTTTGGCT
AAAGATACATTTTTTCCAGCTGCTTATGATAATCCAGAAGATGTTTTGCCTGAGGGGTTCTTGCAAAGGACAGAAGCGAT
TGGGAAGGTGATAGGATGGGCACCCCAGGTGGCTATCTTGAGTCATGATGCTGTAGGTGGCTTTGTGTCACACTGTGGGT
GGAATTTGACTTTAGAGAGCATTTGGTTCGGAGTACCACTGGCAACTTGGCCAATATATTCGGAGCAGCAAGCGAATGCA
TTTCAATTGGTGAAGGATTTAGAGATAGCAGTGGAGATTAAGATGGATTATAGGAAGGATCTCAGGGGGACCGAATCGAA
CGTTATAGTAAAAGCAGAGGAGATAGAGAAAGCAATAAAGCAGTTGATAGATCCTGAAAATGAAATAAGGTTGAAAGTGA
AGGACATGAAGGAGAAGAGCAGATTGGCGCTAAAAGAATGTGGCTCTTCGTACAACTCTGTTGGACATTTTATCGAGCAG
GTGATGGACAAAACTAAGTAA

Alignment

ORF - retro_stub_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKLLITREKNMSITVLIIQSPHDNKLPSYIQSLT---NFSSSLKFIQLPQDDTVLQLRKSNLFTSFIPA
          MAK.LI.R.....ITVL.I..P.DN.L.SYI.S.....N..S..KFI.LPQ....LQ......F..F...
Retrocopy MAKVLIARDEHLVITVLVIKLPSDNMLSSYIESVSTNPNYNSQMKFIELPQYESILQSITNTTFITFLSS

Parental  HKPAVRDVVAEIIKSQSNITLAGIVIDLFCTSMIDVANEFELPTYVFYTCGAAPLGLQFHMQSLSDDFGR
          .KP.VR..V.EI..S.SN..LAG.VID..CT.MIDVANEF.LPTYVFYT.GAA.LGLQ.H.Q.L.DDF..
Retrocopy QKPQVRNSVIEILNSGSN-RLAGLVIDMMCTAMIDVANEFGLPTYVFYTSGAAMLGLQLHLQTLRDDFNQ

Parental  NITNYKDDPEAELSISTYFNPFPAKCLPSVMLDKEGGSTMCLDLTRRFRETKGIMINTFLELDSHAINSL
          ..T.YKDDPEAELS..TY.NPFPAKCLPS...DK.GGSTM.LDL..R.RE.K.I..NTF.E..SHA..SL
Retrocopy DVTEYKDDPEAELSVTTYGNPFPAKCLPSIAFDKDGGSTMYLDLSKRLREAKAILVNTFSEFESHAVKSL

Parental  SRDKNIPPVYPVGPVFNLNSVQGENLSSSD-QNIMKWLDDQPPSSVVFLCFGSGGSFTVEQVKEITYALE
          S.D..IP.VYPVGP..NL....G.N..SS..Q.I..WLDDQP.SSVV.LCFGS.GSF..EQ.KEI.YALE
Retrocopy SLDEKIPLVYPVGPLLNLDNDHGNNQDSSQHQTIINWLDDQPDSSVVYLCFGSLGSFNEEQIKEIAYALE

Parental  NSGCRFLWTLRQPPQKDARLPGDYENFEEVLPEGFLQRTQGIGKVIGWAPQLAILSHRAVGGFVSHCGWN
          .SGCRFLW.L..P..KD...P..Y.N.E.VLPEGFLQRT..IGKVIGWAPQ.AILSH.AVGGFVSHCGWN
Retrocopy KSGCRFLWSLKKPLAKDTFFPAAYDNPEDVLPEGFLQRTEAIGKVIGWAPQVAILSHDAVGGFVSHCGWN

Parental  STLESIYFGVPMATWPMYAEQQANAFQLVKDLEMAVEIKMDYRKEPTGTMGQEVIVKAEEIEKAIRELMD
          .TLESI.FGVP.ATWP.Y.EQQANAFQLVKDLE.AVEIKMDYRK...GT....VIVKAEEIEKAI..L.D
Retrocopy LTLESIWFGVPLATWPIYSEQQANAFQLVKDLEIAVEIKMDYRKDLRGT-ESNVIVKAEEIEKAIKQLID

Parental  PENKIRMKVREMKEKSRATTMEGGSSYTSIGGFIQSIMENTQ
          PEN.IR.KV..MKEKSR....E.GSSY.S.G.FI...M..T.
Retrocopy PENEIRLKVKDMKEKSRLALKECGSSYNSVGHFIEQVMDKTK

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_1 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	PGSC0003DMG400015327	1 retrocopy	retro_stub_1 ,