RetrogeneDB ID: retro_stub_25

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 5:41731286..41732681(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400003352
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400011771
• Aliases: None
• Description: None

Sequence

>retro_stub_25
ATGGCAGACCATGTTTCGTTGAGTGTGCCTGATGAATCCACATGTTTTGATGATGATGGCCGTCCCAAAAGAAGTGGTAC
AGTTTGGACTGCAAGTGCACACATAATAACAGCTGTGATTGGTTCTGGAGTTCTTTCATTAGCTTGGGCTACTGCTCAGC
TTGGATGGATTGCTGGACCTTCTGTTTTGCTACTCTTCTCTGCTGTTACTTACTACACTTGTAGTTTTCTGTCTGATTGT
TATCGTACAGGAGATCAACTTACTGGAAGAAGAAACTATACTTATATGGATGTTGTTCGAAGCAATCTTGGTGATGTTCA
CGTTAAGATTTGTGGGGTTATTCAATACGTAAATCTTGTTGGAGTTGCAATTGGTTACACAATTGCATCTTCTATTAGCA
TGGTTGCAGTAAAAAGATCTAACTGTTTCCACAACAATGGTCATGATCACGCTTCTTGCAATATTTCAAGCACACCCTAC
AAGATCATGTTTGGAGTCTTGGAAATTGTCTTGTCACAAATCCTAAATTTTGATCAGATTTCGTGGCTTTCTATTGCCGC
AGCTCTTATGTCCTTCACTTACAAGACCATTGGGCTTGGCTTAGGAGTTGCCAAAGTTGTACAAACAGGAAAAATACAAG
GGAGTATAAGTACTGGAACTGAAATCGACAAGGTATGGAAAAGCTTTCAAGCTCTTGGAGCTATAGCTTCTGCTTATTCT
TACTCCCTCATCCTTATTGAGATTCAGGATACACTGATCAAATCACCATCAGCAGAAGCAAAGACGATGAAGAAGGCAAC
ACAAATAAGTCTGGTAGTAACAACTGTTCTCTACATGCTCTGTGGCTGCTTTGGCTATGCAGCATTTGGAGACCAATCCC
CAGAAAACCTACTGACTGGATTTGGATTTGACGATCCATATTGGCTACTGGACATCGCAAACGTTGCCGTCGTTATCCAC
CTAGTAGGTGCATATCAAGTTTCCTGCCAAACCCTTTTTGCTTTTGTTGAAAAAAAAGCAGGTGAATGGTACCCAGACAG
CAACATCATCACGACAGAGATCGATATCCCAATCCATCGCTGTAAGCCCTTCAAACTCAACTTTTTCCATCTAATTTGGA
GGACTATTTTTGTGATCGCCACCACTTTCATTTCTGTGCTGATGCCATCCTTTAACAACATCGTTGACATTCTTGGAGCG
TTTGCATTTTGGCCACTTACAGTATACTTCCCAATAAAAATGTACATTGTCAAAAAAAATATTCCCAAATGGAGTGGTAG
GTGGATTTGCCTTCAGTTGCTTAGTGGAGCTTGCCTTGTTATCTCAATTGCTGTAGCTGTTGGTTCTTTTGCTGGACTTG
TTTCTGATTTAAAAGCTTTCAAGCCTTTCAAGTAG

Alignment

ORF - retro_stub_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.09 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HQVFEVYGESKCFDDDGRIKRTGSVWTASAHIITAVIGSGVLSLAWATAQLGWVAGPTVLLLFSFVTYYT
          H....V..ES.CFDDDGR.KR.G.VWTASAHIITAVIGSGVLSLAWATAQLGW.AGP.VLLLFS.VTYYT
Retrocopy HVSLSVPDESTCFDDDGRPKRSGTVWTASAHIITAVIGSGVLSLAWATAQLGWIAGPSVLLLFSAVTYYT

Parental  SALLSDCYRTGDPVTGKRNYTYMDAVRANLGGFQVKICGVIQYANLFGVAIGYTIAASISMVAVNRSNCF
          ...LSDCYRTGD..TG.RNYTYMD.VR.NLG...VKICGVIQY.NL.GVAIGYTIA.SISMVAV.RSNCF
Retrocopy CSFLSDCYRTGDQLTGRRNYTYMDVVRSNLGDVHVKICGVIQYVNLVGVAIGYTIASSISMVAVKRSNCF

Parental  HKQGH-RAACNVSSTPYMIIFGVMEIIFSQIPDFDQISWLSIVAAVMSFTYSTIGLGLGVAQVAETGKIE
          H..GH..A.CN.SSTPY.I.FGV.EI..SQI..FDQISWLSI.AA.MSFTY.TIGLGLGVA.V..TGKI.
Retrocopy HNNGHDHASCNISSTPYKIMFGVLEIVLSQILNFDQISWLSIAAALMSFTYKTIGLGLGVAKVVQTGKIQ

Parental  GSLTGISIGTEVTEMQKIWRSFQALGAIAFAYSYSLILIEIQDTL-KSPPAEAKTMKRATLISVAVTTVF
          GS...IS.GTE.....K.W.SFQALGAIA.AYSYSLILIEIQDTL.KSP.AEAKTMK.AT.IS..VTTV.
Retrocopy GS---ISTGTEI---DKVWKSFQALGAIASAYSYSLILIEIQDTLIKSPSAEAKTMKKATQISLVVTTVL

Parental  YMLCGCFGYAAFGDQSPGNLLTGFGFYNPYWLLDIANVAIVVHLVGAYQVYCQPLFAFVEKTATEWYPDS
          YMLCGCFGYAAFGDQSP.NLLTGFGF..PYWLLDIANVA.V.HLVGAYQV.CQ.LFAFVEK.A.EWYPDS
Retrocopy YMLCGCFGYAAFGDQSPENLLTGFGFDDPYWLLDIANVAVVIHLVGAYQVSCQTLFAFVEKKAGEWYPDS

Parental  KIITKEIDVPIPGFKPFKLNLFRLVWRTIFVIITTVISMLMPFFNDVVGILGAFGFWPLTVYFPVEMYIV
          .IIT.EID.PI...KPFKLN.F.L.WRTIFVI.TT.IS.LMP.FN..V.ILGAF.FWPLTVYFP..MYIV
Retrocopy NIITTEIDIPIHRCKPFKLNFFHLIWRTIFVIATTFISVLMPSFNNIVDILGAFAFWPLTVYFPIKMYIV

Parental  QKRITKWSGRWICLQILSGACLVISIAAAAGSFAGVASDLKVYRPFQ
          .K.I.KWSGRWICLQ.LSGACLVISIA.A.GSFAG..SDLK...PF.
Retrocopy KKNIPKWSGRWICLQLLSGACLVISIAVAVGSFAGLVSDLKAFKPFK

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_25 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400011771	2 retrocopies	retro_stub_25 , retro_stub_56,