RetrogeneDB ID: retro_stub_39

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:67459552..67460821(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400044320
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400025495
• Aliases: None
• Description: None

Sequence

>retro_stub_39
ATGCTTACTTTAAATCTTCTTCCATCCACTAATGTCACTCTCTCCAAATCCCGTCCTAAGTATCCTCTCAGCCCTTCACC
TTTTCATCCAAATCTTGGTAGTAGAAACCAAAAGTTGAGAACTTTGTCATTCACCAAACCCTTGATTCAAAATGGACATC
CTTTTAGGTGTTCTGCAAATCAAGATTCTCAGATCTCTCGTCCAAGATTGGATTTTTCCAAAATCTTGAGACACCCATCT
GGGGTTTCTTCAAGAAATACAACTCAGATCCTTGAAGCAGCATCTGGAACCCCAGAAGAAGTGAGCCCAGATGGGGAGAT
TGAAGTTTCAAAGCCAAAAGTGAATATGAAACTGGCTCTCATTTTTGGTCTGTGGTATTTTCAGAACATTGTGTTTAACA
TATTTAACAAGAAGGTATTGAACATCTTTCCTTATCCATGGCTTCTTGCTTCTTTCCAGCTGTTTTGTGGTTCTGTTTGG
ATGTTAATTCTGTGGTCTTTTAAGCTGCAACCTTGCCCAAAAATCAATAAATCATTTATCATTGCCCTTCTTGGACCTGC
CTTGTTTCACACAATAGGCCATATTTCAGCTTGTGTTTCATTTTCAAAGGTTGCTGTTTCTTTCACCCATGTTATTAAGT
CTGCAGAACCTGTGTTTACTGTGGTGTTTTCATCATTTCTTGGTGATACATATCCTCTGACTGTTTGGCTTTCAATTCTT
CCCATTGTGTTTGGTTGCTCTCTGGCTGCTGTCACTGAAGTGTCCTTCAATTTGGGGGGCTTGTCGGGTGCTATGATCAG
TAATGTTGGGTTTGTTCTTCGCAACATTTTTTCTAAAAGGAGCTTACAGAATTTTAAGGAAGTGGATGGCTTGAACATGT
ATGGATGGATAACCATACTCTCATTTATATATTTATTTCCAGTAGCAGTGTTTGTGGAAGGTTCTCAATGGGTGGCAGGG
TATCACAAAGCTCTTGGAACTATAGGAAATCCTAACACATTTTATTTATGGGTTCTCATATCTGGGATTTTCTATCATCT
CTATAACCAATCTTCTTACCAAGCTCTGGATGATATTAGTCCCCTGACATTTTCAGTGGGTAATACGATGAAGAGAGTTG
TAGTGATTGTCGCCACTGTGTTGGTATTCAGGAATCCAGTCAGGCCTCTAAATGCACTTGGCTCTGCTATTGCCATTTTT
GGAACTTTCTTGTACTCACAGGCAACGGTTAAAAAGCCAAAGAAAGAGGCAGTGGAAAAGAAGGACTAG

Alignment

ORF - retro_stub_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.31 %
• Parental protein coverage: 77.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASRPPISIEFDEETQIVAAH-KFKIGLYFATWWALNVVFNIYNKKVLNAFPFPWLTSTLSLAAGSFIMLV
          AS..P.....D.E..........K..L.F..W...N.VFNI.NKKVLN.FP.PWL.....L..GS..ML.
Retrocopy ASGTPEEVSPDGEIEVSKPKVNMKLALIFGLWYFQNIVFNIFNKKVLNIFPYPWLLASFQLFCGSVWMLI

Parental  SWATRIAETPKTDIDFLKALFPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSSLFLGETFP
          .W.......PK....F..AL...A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.F.V..SS.FLG.T.P
Retrocopy LWSFKLQPCPKINKSFIIALLGPALFHTIGHISACVSFSKVAVSFTHVIKSAEPVFTVVFSS-FLGDTYP

Parental  LPVYLSLVPIIGGCALAAVTELNFNLTGFMGAMISNLAFVFRNIFSKKGMKG-KSVGGMNYYACLSMMSL
          L.V.LS..PI..GC.LAAVTE..FNL.G..GAMISN..FV.RNIFSK......K.V.G.N.Y......S.
Retrocopy LTVWLSILPIVFGCSLAAVTEVSFNLGGLSGAMISNVGFVLRNIFSKRSLQNFKEVDGLNMYGWITILSF

Parental  LILTPFAIAVEGPKVWALGWQNAVSQIG-PN-FIWWVVAQSVFYHLYNQVSYMSLNEISPLTFSIGNTMK
          ..L.P.A..VEG...W..G...A...IG.PN.F..WV.....FYHLYNQ.SY..L..ISPLTFS.GNTMK
Retrocopy IYLFPVAVFVEGSQ-WVAGYHKALGTIGNPNTFYLWVLISGIFYHLYNQSSYQALDDISPLTFSVGNTMK

Parental  RIVVIVSSIIIFQNPIQPVNALGATIAIFGTFLYSQA
          R.VVIV.....F.NP..P.NALG..IAIFGTFLYSQA
Retrocopy RVVVIVATVLVFRNPVRPLNALGSAIAIFGTFLYSQA

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_39 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400025495	1 retrocopy	retro_stub_39 ,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,