RetrogeneDB ID: retro_slyc_36

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:30909487..30911146(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc02g037490.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g031940.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_36
ATGGATCAATTGAAACCAAGTTCTGTCAATTCATCTCCTCTTACACCATTAACATTCTTGGAAAGAGCTGCTGTAGCTTA
TGGGGATAGTGTTTCCATTGTCTGTAACTCCACTACATACACCTGGTCTCAAACATTCACTCGATGTTTACTCCTCGCTT
CCTCAATTTCAACCCTCATTGGTATCAAAAAAGGCCAAGTTGTTTCGGTTTTAGCTCCTAATATTCCCGCAACGTTAGAG
CTTCAATTTGCTGTTCCAATGGCTGGTGCTGTACTCAACAACATCAACACTCGTCTCGATGCCAAAACCGTCTCTGTTCT
GCTCCAACATAGTGAATCGAAGCTCTTGTTTGTTGATTACCAGCTATATCCTTTGGTACTTCAGTCGATTTCATTGTTTC
CATCTGATGTCGACACTCCAATTCTTGTCCTAATAGAAGATGAAAACTCTGTTCCGTTTTCAACAAACTTGGATTTCGAT
CACTGTGATACTTATGATGCTATGTTGGCGAAGGGGGATTTGAATTTCAATTGGATTCGACCTGAGAATGATCGGGATGC
GATGACGTTGAACTACACTTCTGGAACAACATCCTCACCTAAAGGAGTGGTACATTCTCATAGATCTCTTTTTATCATCA
CAGTTGATTCGTTAATAGATTGGTCTGTACCAAGTCAGCCAGTGTATCTATGGACCCTCCCAATGTTCCATTCCAACGGA
TGGAGTTACACATGGGGTATGGCTGTTGTTGGTGGGACCAACATTTGTCTTCGAAAATTCGACGCTAATGTTGTGTTTCA
TGCTATCAACAAATATAATGTCACACATATGTGTGGTGCACCTGTGGTACTCACTATGCTAGCCAATTCCCCCTGTGCTA
AGCCATTACAAAACCCCGTCCACTTCCGTACTGGTGGGGCTCCTCCCCCTGCCACCATTGTCCTTCGTGTCGAATCCTTA
GGATTCATAGTGAATCACGGGTATGGGATGACAGAGGTGGCAGGGGTAGTCGTATCTTGTATTTGGAAACCAAAATGGAA
CAAATTATCTGCGAATGTGAAGGCAAAATTGAAGTCTAGACAAGGGATTAAGAGTTTAGGTATGACGGAGGTTGACGTGG
TGGATCCGGAATCTGGAGTTAGTGTAAAGAGGGATGGCGTTACAATGGGTGAAATTGTATTAAGAGGTGGATGTATAATG
TTGGGTTATTTGAAAAATGAAGAAGCTACATCAAAATGTATGAAAAACAATTGGCTTTATACAGGGGATGTAGCAGTTGT
GCATCCAGATGGGTACTTGGAAATTAAAGATAGATCTAAAGATATTATAATTAGCGGTGGTGAGAATGTAAGCAGTGTTG
AAGTAGAATCCGTACTTTATTCAAACAATTTTGTGAATGAGGCAGCAGTTGTAGCAAGACCCGATGAATTTTGGGGCGAA
ACGCCTTGTGCATTCGTGAGTCTGAAGATGGAACTGAAACTTAAACCGAAAGAGAAGGAAATTATTGATTTCTGTAGAGA
AAGATTGCCACATTATATGATACCCAAGACGGTAATTTTCATGGATGAACTACCCAAAACAGCAACTGGGAAAATTCAAA
AGTTTTCTCTAAGACAGATTGCTAATGGTATGGGGTCGTTACCTGCTAGTCGAATGTAG

Alignment

ORF - retro_slyc_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.92 %
• Parental protein coverage: 87.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KISKGPANTCPFSPLDFLERASIVYGNCTSIVYNDTSYTWSQTYTRCKKLASSISSL-GIKKGDVVSVLS
          .......N..P..PL.FLERA...YG...SIV.N.T.YTWSQT.TRC..LASSIS.L.GIKKG.VVSVL.
Retrocopy QLKPSSVNSSPLTPLTFLERAAVAYGDSVSIVCNSTTYTWSQTFTRCLLLASSISTLIGIKKGQVVSVLA

Parental  PNIPAMYELQFAVPMSGAILNNINFRLDPRTLSVLLRHSESKLVFVDYQASSLLLEAISLFPSNLQRPKL
          PNIPA..ELQFAVPM.GA.LNNIN.RLD..T.SVLL.HSESKL.FVDYQ...L.L..ISLFPS....P.L
Retrocopy PNIPATLELQFAVPMAGAVLNNINTRLDAKTVSVLLQHSESKLLFVDYQLYPLVLQSISLFPSDVDTPIL

Parental  VLIEDNCGDTPLVSRNEF--YNSYENVIDEGDQHFKWIAPESEWEPMTLNYTSGTTYAPKGVLHSHRSAF
          VLIED.....P......F.....Y......GD..F.WI.PE.....MTLNYTSGTT..PKGV.HSHRS.F
Retrocopy VLIEDE-NSVPFSTNLDFDHCDTYDAMLAKGDLNFNWIRPENDRDAMTLNYTSGTTSSPKGVVHSHRSLF

Parental  TMSVMGLIDWSVPKQPVFLWTLPIFHANGWGFCWAMAAVGGTNVCLRRSHDAALIYEAIQQHKVTHMCGA
          ...V..LIDWSVP.QPV.LWTLP.FH.NGW...W.MA.VGGTN.CLR...DA.....AI....VTHMCGA
Retrocopy IITVDSLIDWSVPSQPVYLWTLPMFHSNGWSYTWGMAVVGGTNICLRK-FDANVVFHAINKYNVTHMCGA

Parental  PVVLNMLSTYTKRKPLDSPVQILTAGAPPPAAVLDRTESLGFVISHGYGLTETGGPAVTCAWKQEWNSLT
          PVVL.ML......KPL..PV...T.GAPPPA....R.ESLGF...HGYG.TE..G..V.C.WK..WN.L.
Retrocopy PVVLTMLANSPCAKPLQNPVHFRTGGAPPPATIVLRVESLGFIVNHGYGMTEVAGVVVSCIWKPKWNKLS

Parental  NSERATLKSRQGVKMVGFTDVDVVDPETGISIERNGMAVGEIVLKGGSVMLGYLKDPEGTSKCMKNDGWF
          ....A.LKSRQG.K..G.T.VDVVDPE.G.S..R.G...GEIVL.GG..MLGYLK..E.TSKCMKN..W.
Retrocopy ANVKAKLKSRQGIKSLGMTEVDVVDPESGVSVKRDGVTMGEIVLRGGCIMLGYLKNEEATSKCMKNN-WL

Parental  YTGDVGVMHSDGYLEVKDRSKDVIICGGENISSVEIESILYKHPAVNEAAVVARPDNYWGETPCVFVSLK
          YTGDV.V.H.DGYLE.KDRSKD.II.GGEN.SSVE.ES.LY....VNEAAVVARPD..WGETPC.FVSLK
Retrocopy YTGDVAVVHPDGYLEIKDRSKDIIISGGENVSSVEVESVLYSNNFVNEAAVVARPDEFWGETPCAFVSLK

Parental  NDAR-NVTEKELREFCKENLPLYMVPRTVVIQDDLPKTATGKIQKYLLRDKAKSL
          ........EKE...FC.E.LP.YM.P.TV...D.LPKTATGKIQK..LR..A...
Retrocopy MELKLKPKEKEIIDFCRERLPHYMIPKTVIFMDELPKTATGKIQKFSLRQIANGM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Solanum lycopersicum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum lycopersicum was not studied using ChIP-Seq data.

EST

Solanum lycopersicum was not studied using EST data.

TSS

Solanum lycopersicum was not studied using FANTOM5 data.

Lab

retro_slyc_36 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum lycopersicum 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 lycopersicum	Solyc03g031940.2	1 retrocopy	retro_slyc_36 ,