RetrogeneDB ID: retro_stub_57

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 2:43091845..43094107(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400024970
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400014862
• Aliases: None
• Description: None

Sequence

>retro_stub_57
ATGTCTACATACCCAGTTCTAGTTGTTGTACTTGTGTGCCTATGTCACATGTCTGTGGCAATGGAGGAGAAGAAAACATA
CATCATTCACATGGCTAAATCACAAATGCCAGTAACCTTTGATGACCATACTCACTGGTATGACGCGTCCCTCAAATCGG
TTTCTGAATCAGCAGAGATGATCTATGTTTATAAAAACGTTGTTCATGGTTTTGCAGCAAGGCTTACAGCTCAAGAAGCT
GAATCCTTAGAGACCCAACCTGGGATTCTCTCTGTTTTGCCTGAGGTGATATACCAACTCCACACTACTCGGACGCCTCT
TTTTTTGGGTCTTGATAAAAGTGTTAATATCTTTCCTGAGTCAGATTCTATGAGTGATGTCATCGTCGGAGTACTCGATA
CAGGGGTTTGGCCGGAGAGAAAGAGCTTTGACGATACTGGATTTGGACCTGTTCCAGATTCGTGGAAAGGTCAGTGTGAG
TCCAGCACCAATTTCAGTTCTGCCATGTGTAACAGAAAGCTTGTTGGAGCGAGGTATTTTTCTAGGGGTTATGAAACTAC
TCTTGGACCAATTGATGAGTCCAAGGAGTCTAAATCTCCTAGGGATGATGATGGACATGGAACACACACTGCTTCTACAG
CAGCTGGTTCAGTTGTTCAGGGTGCTAGCCTTTTTGGTTATGCTTCAGGAACTGCTCGTGGAATGGCCTATCATGCCAGA
GTTGCCGTGTACAAAGTTTGCTGGCTTGGGGGATGTTTTAACTCTGACATATTGGCAGGGATGGACAAAGCCATTGATGA
TAAAGTTGATGTGCTTTCATTATCACTTGGTGGAAGCACACCAGATTACTACAAAGACAGCATTGCAATTGGAGCTTTTG
CTGCTATGGAGAAGGGTATTTTGGTTTCTTGCTCTGCTGGAAATGCTGGACCTAATCAATTCAGTTTGTCCAACCAAGCA
CCTTGGATCACCACCGTGGGTGCCGGAACAATTGACCGTGATTTTCCAGCATATGTAAGCCTTGGCAATGGTAAAAATTT
CTCCGGCGTTTCACTTTACGCGGGTGATTCATTACTTAATAAGATGCTTCCCTTGGTGTATGCTGGTAATGCCAGCAATG
TAACCAGTGGAAATCTCTGTATGATGGGTACCTTAATTCCTGAGAAAGTTAAAGGCAAAATTGTGCTGTGTGACAGAGGG
ATTAACGCTCGAGTCCAAAAGGGTTTTGTGGTAAAAGCAGCTGGTGGAGCCGGCATGGTTTTGGCTAACACCGCAGCAAA
TGGGGAGGAGCTAGTGGCTGACGCCCATTTACTTCCAGCGGCGGCGGTGGGTCTAATAGCCGGCGATGCAGTCAAGAAAT
ATTTATTCTCCGATCCTAATCCAACGGCCGAAATTCTTATAGGAGGAACAAAGGTAGGAATCCAACCGTCACCGGTTGTT
GCAGCGTTCAGTTCCAGAGGCCCAAATTCAATCACCCCGGAGATACTCAAACCGGATATTATCGCGCCCGGTGTAAACAT
TCTGGCCGGTTGGACCGGAGCCGTCGGCCCGACGGGGATGGCTGAGGACGATAGACGGGTCGAGTTCAACATTATCTCAG
GCACATCCATGTCGTGTCCACATGTGAGTGGCTTAGCGGCTTTGGTAAAAGGAGTCCACCCAGAATGGAGCCCGGCCGCC
ATTCGTTCGGCGCTCATGACCACCGCTTACACCGTCTACAAGAACGGCGGAGCACTACTAGATGTCGCCACGGGAAAGCC
ATCTACACCTTTCGATCACGGCGCTGGACACGTGGATCCCGTTTCGGCGGTGAACCCAGGTCTTGTTTACGACATAAACG
CCGATGATTACCTCAATTTCATGTGTGCATTGAAATACACTCCATCACAAATCAATAGCTTAGCAAGAAGAAACTTCACA
TGTGATTCAAGCAAAAAATACAGCGTCACAGATTTGAATTACCCTTCCTTTGCTGTTTCATTCCCTGCTGATACCGGTTC
AAACACAATCAAGTACAGCCGGACACTGACTAATGTTGGACCAGCTGGGACATACAAAGTTACTGTTTCTTCCCCTAATA
GTTCAGTGAAAATTATAGTTGAGCCTGAAACAGTGAGTTTCACTCAGATTAATGAGAAGAAATCGTATACTGTGAGTTTT
ACTGCTCCATCAAAGTCCTCATCTACGGATGTATTCGGTAGAATTGAGTGGTCAGATGGGAAGCATGTGGTTAGTAGTCC
AGTTGCAATTTCTTGGTCATGA

Alignment

ORF - retro_stub_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKSQMPEGFEDHTHWYDSSLRSVSASAEMLYVYNNAVHGFAARLTPEEAESLQNQPGILSVLPEMKYEL
          MAKSQMP..F.DHTHWYD.SL.SVS.SAEM.YVY.N.VHGFAARLT..EAESL..QPGILSVLPE..Y.L
Retrocopy MAKSQMPVTFDDHTHWYDASLKSVSESAEMIYVYKNVVHGFAARLTAQEAESLETQPGILSVLPEVIYQL

Parental  HTTRTPLFLGLDVSADYFPESNAMGDVIVGVLDTGVWPESKSFDDNGFGPIPASWKGECESGTNFTSKNC
          HTTRTPLFLGLD.S...FPES..M.DVIVGVLDTGVWPE.KSFDD.GFGP.P.SWKG.CES.TNF.S..C
Retrocopy HTTRTPLFLGLDKSVNIFPESDSMSDVIVGVLDTGVWPERKSFDDTGFGPVPDSWKGQCESSTNFSSAMC

Parental  NRKLIGARYFAKGYESTLGPIDVSKESKSPRDDDGHGTHTSTTAAGSVVQGASLLGYASGNARGMATHAR
          NRKL.GARYF..GYE.TLGPID.SKESKSPRDDDGHGTHT..TAAGSVVQGASL.GYASG.ARGMA.HAR
Retrocopy NRKLVGARYFSRGYETTLGPIDESKESKSPRDDDGHGTHTASTAAGSVVQGASLFGYASGTARGMAYHAR

Parental  VAVYKVCWVGGCFSSDILAGLDKAIDDNVNVLSLSLGGGNSDYYRDSIAIGAFAAMEKGILVSCSAGNAG
          VAVYKVCW.GGCF.SDILAG.DKAIDD.V.VLSLSLGG...DYY.DSIAIGAFAAMEKGILVSCSAGNAG
Retrocopy VAVYKVCWLGGCFNSDILAGMDKAIDDKVDVLSLSLGGSTPDYYKDSIAIGAFAAMEKGILVSCSAGNAG

Parental  PSPYSLSNVAPWITTVGAGTLDRDFPAYVSLGNGKNFSGVSLYKGDSSLSKMLPFVYAGNASNMTNGNLC
          P...SLSN.APWITTVGAGT.DRDFPAYVSLGNGKNFSGVSLY.GDS.L.KMLP.VYAGNASN.T.GNLC
Retrocopy PNQFSLSNQAPWITTVGAGTIDRDFPAYVSLGNGKNFSGVSLYAGDSLLNKMLPLVYAGNASNVTSGNLC

Parental  MTGTLIPEEVKGKIVLCDRGINPRVQKGSVVKAAGGAGMVLANTAANGDELIADAHLIPATSVGQTTGEA
          M.GTLIPE.VKGKIVLCDRGIN.RVQKG.VVKAAGGAGMVLANTAANG.EL.ADAHL.PA..VG...G.A
Retrocopy MMGTLIPEKVKGKIVLCDRGINARVQKGFVVKAAGGAGMVLANTAANGEELVADAHLLPAAAVGLIAGDA

Parental  IKKYLTSDPNPTATILFEGTKVGIKPSPVVAAFSSRGPNSITQEILKPDIIAPGVNILAGWTGAAGPTGL
          .KKYL.SDPNPTA.IL..GTKVGI.PSPVVAAFSSRGPNSIT.EILKPDIIAPGVNILAGWTGA.GPTG.
Retrocopy VKKYLFSDPNPTAEILIGGTKVGIQPSPVVAAFSSRGPNSITPEILKPDIIAPGVNILAGWTGAVGPTGM

Parental  AEDDRRVEFNIISGTSMSCPHVSGLAALLKGAHPDWSPAAIRSALMTTAYTVYKKGGALQDVVTGKPSTP
          AEDDRRVEFNIISGTSMSCPHVSGLAAL.KG.HP.WSPAAIRSALMTTAYTVYK.GGAL.DV.TGKPSTP
Retrocopy AEDDRRVEFNIISGTSMSCPHVSGLAALVKGVHPEWSPAAIRSALMTTAYTVYKNGGALLDVATGKPSTP

Parental  FDHGAGHVDPVAALNPGLVYDLKADDYLNFLCALNYTSIQINSVARRPFSCETSKKFSVADLNYPSFAVV
          FDHGAGHVDPV.A.NPGLVYD..ADDYLNF.CAL.YT..QINS.ARR.F.C..SKK.SV.DLNYPSFAV.
Retrocopy FDHGAGHVDPVSAVNPGLVYDINADDYLNFMCALKYTPSQINSLARRNFTCDSSKKYSVTDLNYPSFAVS

Parental  FPEQMTASSGSGSSSIKHTRTLTNVGPAGTYKVNVISPSNSVKVVVEPEILAFTRMNEQKSYTVTFTAPS
          FP....A..GS....IK..RTLTNVGPAGTYKV.V.SP..SVK..VEPE...FT..NE.KSYTV.FTAPS
Retrocopy FP----ADTGS--NTIKYSRTLTNVGPAGTYKVTVSSPNSSVKIIVEPETVSFTQINEKKSYTVSFTAPS

Parental  MPSTENVYARIEWSDGKHIVSSPVAISWT
          ..S...V..RIEWSDGKH.VSSPVAISW.
Retrocopy KSSSTDVFGRIEWSDGKHVVSSPVAISWS

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_57 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400014862	2 retrocopies	retro_stub_57 , retro_stub_9,
Solanum lycopersicum	Solyc03g044150.2	1 retrocopy	retro_slyc_26,