RetrogeneDB ID: retro_stub_81

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:3871846..3873018(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400013384
• Aliases: None
• Description: None

Sequence

>retro_stub_81
AACAATTCTAAGATCACAGTATACGTGGTGTCTTGTTGGATTTTTGCTGCTTTTGGTGGATTGATGTTTGGTTACGATAT
TGGTATTTCTGGAGGAGTTTCTGCTACGGATGATTTCTTGATTAAATTTTTCCCACATGTTTATCAAACAAAGTTACATG
CTAAAGAAAATAACTATTGCAAATATGATAATTGGCTTCTCCAACTCTTCACTTCATCCTTATACATATCCGCTCTTTTC
GCCAGTTTTTTTTGCTTCAAAAGCCGCTACTAAATTAGGAAGAAAGATAACTATTTTGATCGCGTCAATCTTTTTCATTG
TTGGAGCTGTATTGAGTGCTGTCGCGGAGAACAAGTTGATGCTTATTTTTGGTAGAATTTTGTTTGGTATTGGTGTTGGA
TTCGGAAACGAGACTGTTCCTCTGTTTTTAACTGAAGTTGCACCAATCCAACACAGAGGAGCTGTGAATATCATGTTTCA
ATTGTTTGTGACTATAGGAATATTCATTGCAAATTTTGTTAACTATGGAACTTCAATGATACATCCATATGGTTGGAGAA
TATCACTTGGATTTGCAGCTATTTCCACGGTGATTCTGTTTATTGGTAGTTTTGTGATCACTGACACCCCCTACGAGTCT
AATTGAGCGTGGTAATGAGGAACAGGGGAAGTCCACGCTCGTGAAGATTAGGGGTGTCAGTGATGTTGAGGCTGAGTATA
AAGAAATCGTGGCAGCGTGTGAACATACCAAGCAAGTTAAGCATTCGTTGAAGAATTTACTGAAGCCTGCTAGCATTCCG
CCTCTTGTGATTGGTGTGTTGTTGCAAATCTTTCAGCAATTTACTGGAATCAACGCTATTATGTTTTACGCGCCTGTTCT
GTTTCAGACTATGGGATTCAAGGCCAATGCCTCGCTTCTGTCCTCTGTCATTACTGGAATTGTTAACGTTGGAAGCACAT
TCGTTTCGATCTACCTTGTTGACAAGGTTGGAAGGAGGAAATTGTTCCTCCAATCTTGTTGTCAGATGTTAATTTCTCAG
TTGGCAATCGGTGCAATTTTGGTAACAAGTTTATCGGAGACAGGAACGTTGAACAGGACACTTGCAGCAATAGTGGTGCT
TCTGGTTGTTTAATTCCTAGCGAGACATTCCCATTGGAAACAAGGACAACTG

Alignment

ORF - retro_stub_81 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.08 %
• Parental protein coverage: 79.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NNSKITIYVLSCWIFAAFGGLMFGYDIGISGGVSGMDDFLKKFFPQVYERKSHAKENNYCKYDDQLLQLF
          NNSKIT.YV.SCWIFAAFGGLMFGYDIGISGGVS..DDFL.KFFP.VY..K.HAKENNYCKYD..LLQLF
Retrocopy NNSKITVYVVSCWIFAAFGGLMFGYDIGISGGVSATDDFLIKFFPHVYQTKLHAKENNYCKYDNWLLQLF

Parental  TSSLYLSALVASFF-ASKAATKFGRRPTICMASIFFLAGAVLSAAAKNKLMLIFGRILFGIGVGFGNETV
          TSSLY.SAL.A....ASKAATK.GR..TI..ASIFF..GAVLSA.A.NKLMLIFGRILFGIGVGFGNETV
Retrocopy TSSLYISALFAXXX>ASKAATKLGRKITILIASIFFIVGAVLSAVAENKLMLIFGRILFGIGVGFGNETV

Parental  PLFLTEVAPIQHRGAVNILFQLFVTIGIFIANLVNYGTSMIHPHGWRLSLGFAAVPAIVLLVGSFVITDT
          PLFLTEVAPIQHRGAVNI.FQLFVTIGIFIAN.VNYGTSMIHP.GWR.SLGFAA.....L..GSFVITDT
Retrocopy PLFLTEVAPIQHRGAVNIMFQLFVTIGIFIANFVNYGTSMIHPYGWRISLGFAAISTVILFIGSFVITDT

Parental  P-SSLIERGKDEQGKAALKKIRGVNDVEVEYQEIVAACEQAKLVKHPFRNLAKAASIPPLVISILLQIFQ
          P..SLIERG..EQGK..L.KIRGV.DVE.EY.EIVAACE..K.VKH...NL.K.ASIPPLVI..LLQIFQ
Retrocopy P>TSLIERGNEEQGKSTLVKIRGVSDVEAEYKEIVAACEHTKQVKHSLKNLLKPASIPPLVIGVLLQIFQ

Parental  QFTGINAIMFYAPVLFQTMGFKTDGSLLSSVITGLVNVGSTFVSIYLVDKIGRRKLLLQACCQMLISQLA
          QFTGINAIMFYAPVLFQTMGFK...SLLSSVITG.VNVGSTFVSIYLVDK.GRRKL.LQ.CCQMLISQLA
Retrocopy QFTGINAIMFYAPVLFQTMGFKANASLLSSVITGIVNVGSTFVSIYLVDKVGRRKLFLQSCCQMLISQLA

Parental  IGAILVTNLEETGTLDRKLATIVVFLVCTYVMSFA-WSWGPL
          IGAILVT.L.ETGTL.R.LA.IVV.LV.........W..G.L
Retrocopy IGAILVTSLSETGTLNRTLAAIVVLLVV*FLARHSHWKQGQL

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_81 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	PGSC0003DMG400013384	1 retrocopy	retro_stub_81 ,
Solanum lycopersicum	Solyc03g005140.1	1 retrocopy	retro_slyc_25,