RetrogeneDB ID: retro_stub_22

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 12:49631257..49632349(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400028647
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400010157
• Aliases: None
• Description: None

Sequence

>retro_stub_22
ATGAATTCATCATCGACAGGATTGGAATGGACAGAATGGCTACAAGGATGGCGTCGTTTAACATATGAGACACTTTTTCA
GAAAATCCATGCTAAACATTTACAAGACCCTTTGCTTTTGCCTCCTCTCAATGGCCTAAATTGCATTGTCACAGGAGCCA
CTAGTGGCATTGGACTTGAAATTGCTAAACAATTAGCTGAGTCAGGTGCACATCTTGTTATGGCTGTAAGAAACACAAGT
TTTGCTCATCAACTCATTCAGAAATGGCGAAGAAATGAAACTGAATCGAGGCCTCTAAGCATCGATGTTATAGAGCTTGA
TCTCTTTCATCTCGAATCAGTTGTAAAATTTGCACAAGAATGGAATTCGAGATCAAAACCCCTGCATATTCTCATCAATA
ATGCTGGAATCTATTCTATAGGACAACCACAAAAATTTACCAAAGATGGATATGAAACACATATACAAGTGAACCATCTT
GCCCCTGCATTACTATCTGTTCTGCTTTTGCCTTCTTTGAAAAGAGGCTCTCCGAGCAGGATTATCAATATGAATTCCCT
TATGCATGTAATTGGCGTTGTTGATCCTCAAGATATGAATTTCTTAACCAAGAAGAGTAAGTTCACAAGTAGAAAGGCAT
ACTCGAGTAGCAAATTGGCACAACTGAAGTTTAGCAGTATACTTCAAAAATTTCTAATGAATACTAATATTCATGTAATG
TGCGTAGAGCCAGGAGCTGTACGCACAAATGTTACAAGAGATCTTTCAAGAATTCTGAACATTCTTTATCAGAAAATGTT
CTTTTTCATGTTTGATGCTCAACAGGGTTCAAGAAGTGCACTTTTTGCAGCTACTGATTCTGATAACTTGGATTATTGTG
GTGACTTGAAAGCACAAGGGTGTAATGTTTGTGCCTTCATTGGTTGCCATTGTAGAATTAGTGAACCTAGCAAAGAAGCA
TATAATGAGAGAACTTCTTTTGAAATATGGAATAAGACGATGGAAATGGTTGGTCTTCCTGCAGGTGGTGTTGACATGAT
TCTTCAAGGTGAAGAAATTCATTGCTGCTATGGGGCTAATAGTGATCGTTAA

Alignment

ORF - retro_stub_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.86 %
• Parental protein coverage: 92.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGWMEWLRGWFYLVYEMIFQRILASHLQNPMPLPPINDLTCIVTGSTSGIGREIARQLAEAGAHVVMAVR
          L.W.EWL.GW..L.YE..FQ.I.A.HLQ.P..LPP.N.L.CIVTG.TSGIG.EIA.QLAE.GAH.VMAVR
Retrocopy LEWTEWLQGWRRLTYETLFQKIHAKHLQDPLLLPPLNGLNCIVTGATSGIGLEIAKQLAESGAHLVMAVR

Parental  STNRAQELVRQWQEEWSGKGLPLNIEVMELDLLSLDSVARFAEAWNARMAPVHVLINNAGIFSIGEPQKF
          .T..A..L...W.........PL.I.V.ELDL..L.SV..FA..WN.R..P.H.LINNAGI.SIG.PQKF
Retrocopy NTSFAHQLIQKWRRNET-ESRPLSIDVIELDLFHLESVVKFAQEWNSRSKPLHILINNAGIYSIGQPQKF

Parental  SKDGYEEHMQVNHLAPAMLSILLLPSLIRGSPSRIINVNSTMHYVGFVDPEDMNVVSGKRKYTSVVGYGG
          .KDGYE.H.QVNHLAPA.LS.LLLPSL.RGSPSRIIN.NS.MH..G.VDP.DMN....K.K.TS...Y..
Retrocopy TKDGYETHIQVNHLAPALLSVLLLPSLKRGSPSRIINMNSLMHVIGVVDPQDMNFLTKKSKFTSRKAYSS

Parental  SKLAQIMFSSILHKRLPAESGISVVCNTPGIVLTNVARDLPQFLQVGYRLIPYFIFNAEEGSRSTLFAAT
          SKLAQ..FSSIL.K.L.....I.V.C..PG.V.TNV.RDL...L...Y.....F.F.A..GSRS.LFAAT
Retrocopy SKLAQLKFSSILQKFL-MNTNIHVMCVEPGAVRTNVTRDLSRILNILYQKMFFFMFDAQQGSRSALFAAT

Parental  DPQISEYCEMLKADDWPVCAYISHDCRPTNASEEAHNIETSYKVWEKTLELVGLPSDAVERLIEGEEIKC
          D.....YC..LKA....VCA.I...CR....S.EA.N..TS...W.KT.E.VGLP...V.....GEEI.C
Retrocopy DSDNLDYCGDLKAQGCNVCAFIGCHCRISEPSKEAYNERTSFEIWNKTMEMVGLPAGGVDMILQGEEIHC

Parental  RYGNSQE
          .YG....
Retrocopy CYGANSD

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_22 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400010157	1 retrocopy	retro_stub_22 ,
Populus trichocarpa	POPTR_0015s05560	1 retrocopy	retro_ptri_15,
Solanum lycopersicum	Solyc03g098460.2	1 retrocopy	retro_slyc_7,