RetrogeneDB ID: retro_stub_120

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 5:203283..204528(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400014472
• Aliases: None
• Description: None

Sequence

>retro_stub_120
ATGAGAAATTGGAACTTTCTTGGATTTCTCTGTCTTGCTTTCGTATTGAGAGTTGAATCTTTAAAATTTCATAGGAGTGA
TCAACACGTTGAAAGAATCTCCGGAAGTGCTGGTGATGTGTTGGAGGATGATCCTACAGGTAGGTTGAAAGTTTTTGTAT
ATGAGCTTCCAAGCAAATATAACAAGAAGACTGTGCAGAGGGACTCGCGATGCCTCAGTCACATGTTTGCTGCTGAGATA
TATATGCATCAGTTTCTGTTATCCAGTCCTGTTAGAACACTTGATCCAGAGGAAGCGGATTGGTTTTACACTCCAGTTTA
CACAACTTGTGAGTACTTGACACCACATGGTCATCCTTTACCTTTCAACTCACCACGTATGATGAGAAGCGCGATTCAGC
TTGTTGCTTCTAGCTGGCCATACTGGAACAGGACACAGGGGGCTGATCATTTCTTCATTGTACCACATGATTTTGGTGCA
TGTTTCCATTTTCAAGAAGAGAAAGCTATTGGAAGAGGAATTCTCCCGTTGCTCCAGTGTGCTACCTTGGTTCAAACTTT
TGGACAACGGAATCATGTTTGTTTGAAGGAAGGATCGATAACTATTCCTCCATATGCTCCTCCACGGAAAATTCAATCTC
ACTTGATCTCTCCTGATACTCCAAGATCCATATTTGTCTATTTTCGAGGCTTGTTTTATGACAAAAGAAATGATCCTAAA
GGCGGGTACTATGCAAGAGGTGCTCGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTCTTTGATATTTCTACAGA
TCATCCAACTACATACTACGAAGACATGCAACGAGCTATCTTTTGCTTGTGCCCTCTCGGATGGGCTCCATGGAGTCCTA
GATTGGTTGAAGCTGTTGTATTCGGATGCATCCCCGTTATAATAGCTGATGACATTGTATTGCCATTTGCTGATGCCATT
CCATGGGAAGATATTGGATTGTTTGTAGCGGAGAAGGATGTTCCATATTTGGATAACATTCTTACTTCTGTTCCACCACA
AGAAATACTGAGGAAGCAGAGATTGCTTGCCAATCCTTCAATGAAGCAGGCTATGTTATTTCTACAACCTGCTCAACCAG
GTGATGCTTTCCACCAAATCTTGAATGGACTTGCTCGTAAATTACCCCATCATTACAAGACCATATACGGAGACAACAAC
GTCTTAAACTGGACTGCTGGTCCAGTTGGTGATCTAAAACCTTGG

Alignment

ORF - retro_stub_120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRNWSWGFLVLLHLAFLLGTEAFKFHKT-QRTERISGSAGDVLEDDPVGRLKVFVYELPSKYNKKILQKD
          MRNW...FL..L.LAF.L..E..KFH...Q..ERISGSAGDVLEDDP.GRLKVFVYELPSKYNKK..Q.D
Retrocopy MRNWN--FLGFLCLAFVLRVESLKFHRSDQHVERISGSAGDVLEDDPTGRLKVFVYELPSKYNKKTVQRD

Parental  PRCLSHMFAAEIYMHRFLLSSPVRTLNPEEADWFYTPVYTTCD-LTPNGLPLPFKSPRMMRSAIQLIASN
          .RCLSHMFAAEIYMH.FLLSSPVRTL.PEEADWFYTPVYTTC..LTP.G.PLPF.SPRMMRSAIQL.AS.
Retrocopy SRCLSHMFAAEIYMHQFLLSSPVRTLDPEEADWFYTPVYTTCEYLTPHGHPLPFNSPRMMRSAIQLVASS

Parental  WPYWNRTEGADHFFIVPHDFAACFHYQEEKAIGRGILPLLQRSTLVQTFGQRNHVCLKDGSITIPPYAPP
          WPYWNRT.GADHFFIVPHDF.ACFH.QEEKAIGRGILPLLQ..TLVQTFGQRNHVCLK.GSITIPPYAPP
Retrocopy WPYWNRTQGADHFFIVPHDFGACFHFQEEKAIGRGILPLLQCATLVQTFGQRNHVCLKEGSITIPPYAPP

Parental  QKMQSHFIPPDIPRSIFVYFRGLFYDVGNDPEGGYYARGARAAVWENFKDNPLFDISTEHPTTYYEDMQR
          .K.QSH.I.PD.PRSIFVYFRGLFYD..NDP.GGYYARGARAAVWENFKDNPLFDIST.HPTTYYEDMQR
Retrocopy RKIQSHLISPDTPRSIFVYFRGLFYDKRNDPKGGYYARGARAAVWENFKDNPLFDISTDHPTTYYEDMQR

Parental  AIFCLCPLGWAPWSPRLVEAVIFGCIPVIIADDIVLPFADAIPWEEIGVFVAEKDVPNLDTILTSIPPEE
          AIFCLCPLGWAPWSPRLVEAV.FGCIPVIIADDIVLPFADAIPWE.IG.FVAEKDVP.LD.ILTS.PP.E
Retrocopy AIFCLCPLGWAPWSPRLVEAVVFGCIPVIIADDIVLPFADAIPWEDIGLFVAEKDVPYLDNILTSVPPQE

Parental  ILRKQRLLANPSMKQAMLFPQPAQSGDAFHQILNGLARKLPHDRSVYLTPGEKILNWTAGPVGDLKPW
          ILRKQRLLANPSMKQAMLF.QPAQ.GDAFHQILNGLARKLPH............LNWTAGPVGDLKPW
Retrocopy ILRKQRLLANPSMKQAMLFLQPAQPGDAFHQILNGLARKLPHHYKT-IYGDNNVLNWTAGPVGDLKPW

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_120 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538848.1_FG012	1 retrocopy	retro_olon_4,
Oryza brachyantha	OB01G51480	1 retrocopy	retro_obra_20,
Solanum tuberosum	PGSC0003DMG400014472	1 retrocopy	retro_stub_120 ,
Solanum lycopersicum	Solyc12g042360.1	1 retrocopy	retro_slyc_19,