RetrogeneDB ID: retro_stub_58

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:66368845..66369670(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400004929
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400003635
• Aliases: None
• Description: None

Sequence

>retro_stub_58
ATGCCTCAAAGCTCATCAACAAAGACGCACGATCAAGATCCGACGGACATTACCGGACCCACCCTAAAATCACAGCGTAC
CAAAATGGTGAATACTTCCGATGACAGTGAAAAAAAGAGTTCTGGTAAGAAGCTGAAAGAGCTTGAAGTTGGTGTTCCAA
TAGTGTATGGAAATGTTGCATTTTGGCTTGGTAAGAAGGCGAGCGAGTTCCAGTCTCATAAATGGACTATTTATGTTCGT
GGTGCAACTAATGAGGATCTGGGTGTGGTGGTGAAACGTGTTGTTTTTCAATTGCACTCAAGTTTTAACAATCCTACAAG
GGTTGTGGACAACCCTCCTTTTGAGTTAACAGAATCTGGATGGGGTGAATTTGAAATTGTGATGACCCTTCATTTCCACA
CTGATGTTTGTGATAAGCCATTACACTTATATCACCATTTGAAACTATATCCAGAGGACGAATCTGGGGCTCTATCCACT
AAAAAACCTGTTGTAGTAGAGTCGTATGATGAAATTGTGTTTGCGGAGCCTTCAGAATCTTTTTTTGCCCGTGTACAGAA
CCATCCAGCAGTCAATGTGCCTAGACTACCTCCTGGCCTAAATTTGCCTCCTCCTGTACCTATAGAAGATGTTGATCGAA
GGAAACGTGGTGACACCAAAGATCATCCTCTAAGTCAATTGTTCACAAACTTTTCCGAAGCAGACGAATTGTTAAAACTT
ACAGCAGCTCGGCAGCAGGTGCAAGGTCATATCGCAAGATTGAGAAGACAGTTGAGCATGGTAGATGGTCAGCATCAACA
ATTGAAGCCTGCCTCTGATCTGTGA

Alignment

ORF - retro_stub_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPLNSPSMTPNDSDLGGNDADPRLQLTKIANPSEDFEKKTSCKRLKDVEIYVPIVFGTIAFWLGKKATET
          MP..S...T...............Q.TK..N.S.D.EKK.S.K.LK..E..VPIV.G..AFWLGKKA.E.
Retrocopy MPQSSSTKTHDQDPTDITGPTLKSQRTKMVNTSDDSEKKSSGKKLKELEVGVPIVYGNVAFWLGKKASEF

Parental  QSHRWSVYVRGATNEDLSGVIKKVVFQLHPSFNNPVRVVESPPFELSECGWGEFEIAISLLFHDDVGEKK
          QSH.W..YVRGATNEDL..V.K.VVFQLH.SFNNP.RVV..PPFEL.E.GWGEFEI...L.FH.DV..K.
Retrocopy QSHKWTIYVRGATNEDLGVVVKRVVFQLHSSFNNPTRVVDNPPFELTESGWGEFEIVMTLHFHTDVCDKP

Parental  LDLYHHLKLYAENEPGPQSTKKPIVVETYNEIVFPDPPEDFFSRIQNHPAVVVPRLPATFKL-PPAPIED
          L.LYHHLKLY.E.E.G..STKKP.VVE.Y.EIVF..P.E.FF.R.QNHPAV.VPRLP....L.PP.PIED
Retrocopy LHLYHHLKLYPEDESGALSTKKPVVVESYDEIVFAEPSESFFARVQNHPAVNVPRLPPGLNLPPPVPIED

Parental  LHALKRGDTKNHPLSQWFINFSEADELLKLTAARQRVQAHIVKLRRQLSVMDELPQTFKLDSD
          ....KRGDTK.HPLSQ.F.NFSEADELLKLTAARQ.VQ.HI..LRRQLS..D...Q..K..SD
Retrocopy VDRRKRGDTKDHPLSQLFTNFSEADELLKLTAARQQVQGHIARLRRQLSMVDGQHQQLKPASD

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_58 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	PGSC0003DMG400003635	1 retrocopy	retro_stub_58 ,