RetrogeneDB ID: retro_slyc_32

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 1:80601571..80602840(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc01g081390.2
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g064270.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_32
ATGCTTACTTTAAATCTTCTTCCATCCACTAATGTCACTCTCTCCAAATCCCGTCCTAACTATCCTGTTAGCCCTTCACC
TTTTCAACCAAATCTTGGTAGTAGAAACCAAAAGTTGAGAACTTTGTCATTCACCAAACCCTTGATTCAAAATGGACACC
CTTTCAGGTCTTCTGCAAATCAAGATTCTCAGATCTCTGGTCCAAGATTGGATTTTTCCAGAATCTTGAGACACCCATCT
GGGGTTTCTTCAAGAAATACAACTCAGATCCTTGAAGCAGCATCTGGAACCCCAGAAGAAGTGAGTCCAGATGGGGAGAT
TGAAGTTTCAAAGCCAAAAGTTAATATGAAACTGGTTCTCATTTTTGGTCTGTGGTATTTTCAGAACATTGTGTTTAACA
TATTTAACAAGAAGGTATTGAACATCTTCCCTTATCCATGGCTTCTTGCTTCTTTCCAGCTGTTTTGTGGTGCTGTTTGG
ATGTTAATTCTGTGGTCTTCTAAGCTGCAACCTTGTCCAAAAATCAATAAATCGTTTATCATTGCCCTTCTTGGACCTGC
CTTATTTCACACAATAGGCCATATTTCAGCTTGTGTTTCATTTTCAAAGGTGGCTGTTTCTTTCACTCATGTTATTAAGT
CTGCAGAACCTGTGTTTACTGTTGTGTTTTCATCGTTCCTTGGTGATACATATCCTCTGACTGTTTGGCTTTCAATTCTT
CCCATTGTGTTTGGTTGCTCCCTGGCTGCAGTCACTGAAGTGTCCTTCAATTTTGGGGGCTTGTCGGGTGCTATGATCAG
TAATGTTGGGTTTGTTCTTCGCAACATTTTTTCAAAAAGGAGCTTACAGAACTTTAAGGAAGTGGATGGCTTAAACCTGT
ATGGATGGATAACCATAATCTCATTTATATATTTATTTCCAGTAGCAGTGTTTGTGGAAGGTTCTCAATGGGTGGCAGGG
TATCACAAAGCTCTTGGAACTATAGGAAATCCTAACACATTTTATTTATGGGTTCTCATATCTGGGATTTTCTATCATCT
CTACAACCAATCCTCTTACCAAGCTCTGGATGATATTAGTCCCCTGACGTTTTCAGTGGGTAATACTATGAAGAGAGTGG
TGGTGATTGTCGCCACTGTGTTGGTATTCAGGAATCCAGTCAGGCCTCTAAATGCACTTGGCTCTGCTATTGCCATATTT
GGAACTTTCTTGTACTCACAGGCAACGGTTAAAAAGCCAAAGAAAGAGGCAGTGGAAAAGAAGGACTAG

Alignment

ORF - retro_slyc_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.04 %
• Parental protein coverage: 78.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EADRAEPME-GPESKAELAR---KMKIGVYFATWWFLNVIFNIYNKKVLNAFPFPWLTSTLSLAAGSLIM
          EA....P.E..P....E.......MK....F..W.F.N..FNI.NKKVLN.FP.PWL.....L..G...M
Retrocopy EAASGTPEEVSPDGEIEVSKPKVNMKLVLIFGLWYFQNIVFNIFNKKVLNIFPYPWLLASFQLFCGAVWM

Parental  LISWTLRIAEAPKTDLEFWKTLLPVAIAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRFLLGES
          LI.W.......PK....F...LL..A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.F.V..S.F.LG..
Retrocopy LILWSSKLQPCPKINKSFIIALLGPALFHTIGHISACVSFSKVAVSFTHVIKSAEPVFTVVFSSF-LGDT

Parental  FPTAVYLSLIPIIGGCGLSALTELNFNWIGFSGAMISNVAFVFRNIFSKKGMKG-KSVSGMNYYACLSML
          .P..V.LS..PI..GC.L.A.TE..FN..G.SGAMISNV.FV.RNIFSK......K.V.G.N.Y......
Retrocopy YPLTVWLSILPIVFGCSLAAVTEVSFNFGGLSGAMISNVGFVLRNIFSKRSLQNFKEVDGLNLYGWITII

Parental  SLLILTPFAIAVEGPQMWALGFEKAVSQIG-PQIVW-WMAAQSVFYHLYNQVSYMSLDEISPLTFSIGNT
          S...L.P.A..VEG.Q.W..G..KA...IG.P.....W......FYHLYNQ.SY..LD.ISPLTFS.GNT
Retrocopy SFIYLFPVAVFVEGSQ-WVAGYHKALGTIGNPNTFYLWVLISGIFYHLYNQSSYQALDDISPLTFSVGNT

Parental  MKRISVIVSSIIIFRTPVQPVNALGAAIAILGTFLYSQA
          MKR..VIV.....FR.PV.P.NALG.AIAI.GTFLYSQA
Retrocopy MKRVVVIVATVLVFRNPVRPLNALGSAIAIFGTFLYSQA

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_32 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Solanum lycopersicum	Solyc07g064270.2	1 retrocopy	retro_slyc_32 ,