RetrogeneDB ID: retro_stub_33

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 12:11429704..11432173(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400002239
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG402024649
• Aliases: None
• Description: None

Sequence

>retro_stub_33
ATGGAGAAATCGAGCCCAACGCTTGAGAGCAGAAAGAGGAAGACAGCCGGTGAAGACGAAGACGAAGATGTTAAGTTCAA
GGGAAAGCGTACTGAACAAGTTGAAAAATTAAGGAAAGTTTCAAGGCAGGAGTATTTGAAGAATAGGGAGAAGAAGAAAT
TAAAGCAACTCAGAGATGATATAGAAGATGAGCAATTTTTGTTTGAGAAAATCGAAAAATTGAGCGAACCAGAAAAACGT
GAACATTTATACAAGCAACAAATTGTTGAATTGGTTAGTAAGGAGCAGCAGTGCGACGACGCCGGTGAGGAACGTGAGAT
TCATCCACAACAAGCTTGGGAGGAAAATCAGATCAGCAATGCGAAACTTAATTTTGGATCTAAAGACAGAAAACAGAAGG
ATTATCAATTTGTGTTTGAAGATCAAATTGAATTCATCAAATCAACTATAATTGATTCAGATTCAGATGTTGATAATGAG
AAGCTGCAATGTACCAGAAATTCGAAACTTAACGAGGATAGGAAGGATTTACCAATTTATCCGTACAAGGATGCTTTGCT
CCAAGCTGTTCATGATCATCAAGTTCTTATCATAGTTGGAGAAACTGGCTCCGGGAAGACAACTCAAATACCTCAATATC
TACATGAAGCAGGTTTTACTAGAAGCGGTGGGAAGATGATTGGTTGTACTCAGCCTCGAAGAGTTGCGGCAATGAGAGTT
GCTGCGCGTGTTTCACATGAAATGGGGGTTAAACTTGGTCATGAGGTTGGTTATTCTATTCGTTTCGAGGATTGTACTTC
TGAGAAAACTATTCTCAAGTATATGACTGACGGAATGTTGCTGAGAGAGTTCCTTACCGAGCCTGATTTAGCAAGCTATA
GTGTTATAATGATTGACGAGGCTCATGAAAGAACATTGTCAACGGATATCCTGTTTGGGTTAATAAAAGATGTAGCTCGT
GCTCGACCCCGACTCAAGTTACTTATATCTAGCGCCACCCTTGATGCAAAGAAGTTTAGTGATTATTTTGACCGTGCTCC
GATTTTTAATATACCTGGAAGGCGATTTCCGGTTGAGAAACATCATTCAAAAGCACCAATCTCTGATTACTTGGATGCAG
CAGTAGTTACTGCACTTCAGATTCATGCAACTCAACCACAGGGTGATGGTGATATATTAATCTTTTTGACGGGGCAGGAG
GAGATTGAAACAGCTGAGAATATTATTAATCGCCGAATAAGAGCTTTGGGAACGAAAATAGCTGAGTTGATAACCTGTCC
AATATATGCAAACTTACCAACTGAACTACAAGCCAAGATATTTGAGCCTACTCCTGAAGGGGTTCGTAAAGTTGTCCTGG
CTACAAATATAGCAGAGACATCATTGACGATTGATGGAATCAAGTATGTTATTGATACAGGGTTTTGTAAGATCAATTGT
TACAACCCTCGAACAGGAACTGAGTCATTGATGGTTGCTCCTATCTCGAAGGCATCTGCCAACCAACGTGCTGGTCGATC
AGGACGAACAGGTCCTGGAAAGTGCTTCCGGTTATATACTGAACATAGCTACATGAATGATTTGGAAGATAACACAATTC
CAGAAATACAAAGGACTAACCTTGCAAATGTCGTGCTCTTACTCAAGAGTGTAGGGATTACCGACTTGCTGAACTTTGAC
TTCATGGATCCTCCACCAGCTGAAGCTCTACTTAAAGCCCTGGAATTGTTATTTGCACTTGGTTCCCTTGATAAGGATGG
TAAGTTAACCAAAGTGGGTGAAAGAATGTCCGAGTTTCCTTTGGATCCAATGCTTTCCAAGATGATAGTTGCATCTGATA
AGTACAAGTGCTCAGCTGAGATAATAAGTATTGCTGCAATGCTTTCTGTCGGGAATTCAATCTTCTATCGTCCAAAGGAC
AGACAAGTCCAAGCTGACAATGCGTGGATGAACTTTCATGTTGGCAATGTGGGAGATCATATTGCTTTGCTTAAGGTTTA
CAATTCCTGGAAGGAAACAAAATTTTCAACTCAGTGGTGCTATGAGAATTACATCCAGGTCAGAAGCATGAAAAAAGCTA
GAGATATCCGAGATCAGTTAGAAGGTCGGCTTGAAAGGGTTGGAATTGATTTGACTTCAAATGTTAATGACTTGGAAGCT
ATTAAGAAGTCTATAATATCAGGATTTTTTCCCCACTCAGCAAGGCTACAGAAGAATGGAGCTTATCGAACTGTTAAACA
TCCCCAGACAGGTCACATTCATCCCAGCTCGGGTTTATCACAGGTACTTCCTAGATGGGTTGTCTACCATGAGCTGGTCC
TGACAACTAAGGAGTACATGCGGCAGGTATCTGAATTGAAACCAGAATGGCTTGTAGAAGTAGCTCCTCACTATTATCAG
TTGAAAGACGTTGAAGACTCAAGCTCGAAGAAAATGCCTCGTGGAATTGGCCTTGCATCTTCTAAATAG

Alignment

ORF - retro_stub_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.23 %
• Parental protein coverage: 73.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDQEPSIDSIEKTMAKSAFEKLQEDRKTLPMYPYRDDLLQAINDHQVLVIVGETGSGKTTQIPQYLHEAG
          .D.....D............KL.EDRK.LP.YPY.D.LLQA..DHQVL.IVGETGSGKTTQIPQYLHEAG
Retrocopy IDSDSDVDNEKLQCTRNS--KLNEDRKDLPIYPYKDALLQAVHDHQVLIIVGETGSGKTTQIPQYLHEAG

Parental  YTKRG--KIGCTQPRRVAAMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFLGEP
          .T..G...IGCTQPRRVAAM.VAARVS.EMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFL.EP
Retrocopy FTRSGGKMIGCTQPRRVAAMRVAARVSHEMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFLTEP

Parental  DLASYSVIMVDEAHERTLSTDILFGLVKDISRFRPDLKLLISSATLDAEKFSDYFDCAPIFKIPGRRFPV
          DLASYSVIM.DEAHERTLSTDILFGL.KD..R.RP.LKLLISSATLDA.KFSDYFD.APIF.IPGRRFPV
Retrocopy DLASYSVIMIDEAHERTLSTDILFGLIKDVARARPRLKLLISSATLDAKKFSDYFDRAPIFNIPGRRFPV

Parental  EIHYTKAPEADYLDAAVVTALQIHVTQPPGDGDILIFLTGQEEIETAEEIIKHRIKGLGTKIAELIICPI
          E.H..KAP..DYLDAAVVTALQIH.TQP.GDGDILIFLTGQEEIETAE.II..RI..LGTKIAELI.CPI
Retrocopy EKHHSKAPISDYLDAAVVTALQIHATQPQGDGDILIFLTGQEEIETAENIINRRIRALGTKIAELITCPI

Parental  YANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVIDPGFSKMKSYNPRTGMESLLVAPISKA
          YANLPTELQAKIFEPTPEG.RKVVLATNIAETSLTIDGIKYVID.GF.K...YNPRTG.ESL.VAPISKA
Retrocopy YANLPTELQAKIFEPTPEGVRKVVLATNIAETSLTIDGIKYVIDTGFCKINCYNPRTGTESLMVAPISKA

Parental  SANQRAGRSGRTGPGKCFRLYTAYNYMNDLEDNTVPEIQRTNLANVVLSLKSLGIHDLLNFDFMDPPPAE
          SANQRAGRSGRTGPGKCFRLYT...YMNDLEDNT.PEIQRTNLANVVL.LKS.GI.DLLNFDFMDPPPAE
Retrocopy SANQRAGRSGRTGPGKCFRLYTEHSYMNDLEDNTIPEIQRTNLANVVLLLKSVGITDLLNFDFMDPPPAE

Parental  ALLKALELLFALSALNKLGELTKVGRRMAEFPLDPMLSKMIVASDKYKCSDEIISIAAMLSVGNSIFYRP
          ALLKALELLFAL..L.K.G.LTKVG.RM.EFPLDPMLSKMIVASDKYKCS.EIISIAAMLSVGNSIFYRP
Retrocopy ALLKALELLFALGSLDKDGKLTKVGERMSEFPLDPMLSKMIVASDKYKCSAEIISIAAMLSVGNSIFYRP

Parental  KDKQVHADNARMNFHVGNVGDHIALLKVYSSWRETDFSTQWCYENYIQVRSMKRARDIRDQLEGLLERVE
          KD.QV.ADNA.MNFHVGNVGDHIALLKVY.SW.ET.FSTQWCYENYIQVRSMK.ARDIRDQLEG.LERV.
Retrocopy KDRQVQADNAWMNFHVGNVGDHIALLKVYNSWKETKFSTQWCYENYIQVRSMKKARDIRDQLEGRLERVG

Parental  IELTSNDNDYEAIKKAITSGFFPHSAKLQKNGSYRTIKHPQTVNVHPSSGLAQVLPRWVVYHELVLTTKE
          I.LTSN.ND.EAIKK.I.SGFFPHSA.LQKNG.YRT.KHPQT...HPSSGL.QVLPRWVVYHELVLTTKE
Retrocopy IDLTSNVNDLEAIKKSIISGFFPHSARLQKNGAYRTVKHPQTGHIHPSSGLSQVLPRWVVYHELVLTTKE

Parental  YMRQVTELKPDWLVEIAPHYYQLKDVEDSSSKKMPRGTGRAS
          YMRQV.ELKP.WLVE.APHYYQLKDVEDSSSKKMPRG.G.AS
Retrocopy YMRQVSELKPEWLVEVAPHYYQLKDVEDSSSKKMPRGIGLAS

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_33 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33 ,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,