RetrogeneDB ID: retro_stub_48

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:62276564..62277971(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400027554
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400017413
• Aliases: None
• Description: None

Sequence

>retro_stub_48
ATGGGATCATTGGTTGATAGTGTTGCAGTGCATAACTTGAACAAGAAGATTGTGATGGGTGACAATGGTTATGTTCTGGA
AGACGTTCCTCATTTGTCTGATTATATTCCTAGTCTTCCTACGTATCCTAATCCATTGAAGAACAATCCTTCCTATTCAG
TCGTTAATCAGTATTTTGTCGATAAAGATGATACAGTTGCTCAAAACATTGTTGTCCGCAAGAATAGTCCAAGAGGGATA
CATTTTCGTCGAGCTGGTCCTTCCCAAAACGTTTATTTTAAGTCCGACGATGTTAATGCATGTATTGTAACATGTGGAGG
TTTATGTCCTGGTCTTAACACAGTTATCAGGGAAATAGTATGTGGCCTATACTCTATGTATGGTGTAAGAAGAGTGATGG
GGATAGATGGAGGATATCAAGGTTTCTATTCCAAAAACACGATTCCTTTGACACCTAAGGTTGTGAATGATATCCATAAA
CGTGGTGGAACGATTCTTGGGTCATCTCGAGGAGGTCATGTTACGAAGAAAATAGTTGATAGCATTCAGGACCGGGGTAT
CAATCAGGTTTATATAATTGGAGGAGATGGAACACAGAAAGGAGCATCGGTGTTATTTGAGGAAATTACAAGGCGTGGTC
TGAATGTTGCAGTTGTTGGAATCCCCAAGACAATCGATAATGATATACCAATTATTGACAAGTCTTTTGGTTTTGATTCC
GCGGTTGAGGAAGCTCAACGTGCTATTAATGCTGCTCATGTTGAAGCTACGAGTTTTGAGAATGGAATTGGGGTTGTGAA
GTTAATGGGACGGGATAGTGGGTTCATAGCAATGTATGCTAGTCTTGCTAGTGGAGATGTTGATTGTTGTTTGATTCCAG
AATCTGATTACTATCTTGAAGGACGTGGTGGAGTGTTTGAGTACATAGAACAAAGGCTCAAAGAGAATGGACACATGGTT
ATAGTTGTAGCTGAAGGTGCCGGACAAGAAGTTGATGTTGGTTTATGGATATCGAAAAGGATAAAGGAGCATTTTTTGAA
AGAAAAGAAGATGATGATCAATCTTAAATATATAGATCCGACATACATGATTCGGGCTATTGCAAGTAATGCATCTGATA
ATGTGTATTGCACACTTCTTGCTCAAAGTGCTGTACATGGAGCAATGGCTGGCTACACAGGCTTTACGGTTGGTCCTGTC
AACAACACACATGCTTACATACCCTTTGATAGAATCACTGAGAAACAAAACAAGGTTGACATTACAGACATGATGTGGGC
ACAACTTCTATCTTCAACAAATCAACCTAGCTTCTTGTCAACAACGAGATCAGCCGATATAATTGAAGCAAACAAGGGCG
AAGAACCACCTACTCAATTATCAGACGAAGAAACAAATCCTTGCTAA

Alignment

ORF - retro_stub_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 62.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKIVIGDDGYVLEDVPHLSDYIPNLSTYTNPLQHNPSYSVVKQYFVDEDDTVAEKVVVHKNSPRGLHFRR
          KKIV.GD.GYVLEDVPHLSDYIP.L.TY.NPL..NPSYSVV.QYFVD.DDTVA...VV.KNSPRG.HFRR
Retrocopy KKIVMGDNGYVLEDVPHLSDYIPSLPTYPNPLKNNPSYSVVNQYFVDKDDTVAQNIVVRKNSPRGIHFRR

Parental  AGPCQKVYFEPDDVYACIVTCGGLCPGLNTVIREIVCGLHYMYGVSRVMGIDGGYRGFYSKNTIPLTPKV
          AGP.Q.VYF..DDV.ACIVTCGGLCPGLNTVIREIVCGL..MYGV.RVMGIDGGY.GFYSKNTIPLTPKV
Retrocopy AGPSQNVYFKSDDVNACIVTCGGLCPGLNTVIREIVCGLYSMYGVRRVMGIDGGYQGFYSKNTIPLTPKV

Parental  VNDIHKRGGTILGTSRGGHVTKKIVDSIQDRGINQVYIIGGDGTQRGAAVIFEEIRRRGLNVAVAGIPKT
          VNDIHKRGGTILG.SRGGHVTKKIVDSIQDRGINQVYIIGGDGTQ.GA.V.FEEI.RRGLNVAV.GIPKT
Retrocopy VNDIHKRGGTILGSSRGGHVTKKIVDSIQDRGINQVYIIGGDGTQKGASVLFEEITRRGLNVAVVGIPKT

Parental  IDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIGLVKLMGRDSGFIAMYATLASRDVDCCLIPE
          IDNDIP.IDKSFGFDSAVEEAQRAI.AAHVEATSFENGIG.VKLMGRDSGFIAMYA.LAS.DVDCCLIPE
Retrocopy IDNDIPIIDKSFGFDSAVEEAQRAINAAHVEATSFENGIGVVKLMGRDSGFIAMYASLASGDVDCCLIPE

Parental  SPFYLEGSGGLFEYIEHRLKDNGHMVIVIAEGAGQEL
          S..YLEG.GG.FEYIE.RLK.NGHMVIV.AEGAGQE.
Retrocopy SDYYLEGRGGVFEYIEQRLKENGHMVIVVAEGAGQEV

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_48 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400017413	1 retrocopy	retro_stub_48 ,
Solanum lycopersicum	Solyc07g045160.2	1 retrocopy	retro_slyc_27,