RetrogeneDB ID: retro_olon_6

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN539477.1:66189..67011(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN539477.1_FG008
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN539056.1_FG008
• Aliases: None
• Description: None

Sequence

>retro_olon_6
ATGCAGGGGAACCGGGAGTTCCTGGTGGAGGTGCTGATGCTGAGCCTGCTGGCGGAGCACCCAAACCTGGTGACGCTGCT
GGGTTACTGCTCCGACGGCGACCACCGCATCCTGGTGTACGAGTACATGGCCCGCGGCTCCCTGGAGGACCACCTGCTCG
ACCTGCCCCCTGGCGCCGCCGCTCTGGACTGGACCACTCGGATGCGCATCGCCCAGGGCGCCGCCCGCGGCCTCGAGCAC
CTGCACGACGCTGCTCGCCCCCCCGTCATCTACCGCGACTTCAAGGCCTCCAACATCCTCCTCGACTCCTCCTTCCAGGC
CCGCCTCTCCGACTTCGGCCTCGCCAAGGTCGGCCCCGTCGGCGACAAGACCCACGTCTCCACCCGCGTCATGGGCACCT
ACGGCTACTGCGCCCCCGAGTACGCTCTCACCGGCAAGCTCACCACCTGCTCCGACGTCTACAGCTTCGGCGTCGTCTTC
CTCGAGATCATCACCGGCCGCCGCGCCATCGACATGGCCCGCCCTCACGATGAGCAGAACCTCGTCCAGTGGGCCGCCCC
GCGCTTCAAGGACAAGAAGCTCTTCGCCGACATGGCCGACCCCTTGCTCCGCGGCGCCTACCCCACCAAGGGCCTCTACC
AGGCGCTCGCCATCGCCGCCATGTGCCTCCAGGAGGACGCCACCATGCGCCCTGCCATCAGCGACGTCGTCACCGCGCTC
GAGTACCTCACCGTCGCCGGCGCCTCCTCCGAGCCTGCCCCTCGTCCCCAGAAGCTACAGCCGCCGGAGGACGACGACGA
TGACCAACGCCCCGCCGCATAA

Alignment

ORF - retro_olon_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQGNREFLVEVLMLSLL-HHQNLVNLIGYCADGDQRLLVYEYMHFGSLEDHLHDLPPDKEALDWNTRMKI
          .QGNREFLVEVLMLSLL..H.NLV.L.GYC.DGD.R.LVYEYM..GSLEDHL.DLPP...ALDW.TRM.I
Retrocopy MQGNREFLVEVLMLSLLAEHPNLVTLLGYCSDGDHRILVYEYMARGSLEDHLLDLPPGAAALDWTTRMRI

Parental  AAGAAKGLEYLHDKANPPVIYRDFKSSNILLDESFHPKLSDFGLAKLGPVGDKSHVSTRVMGTYGYCAPE
          A.GAA.GLE.LHD.A.PPVIYRDFK.SNILLD.SF...LSDFGLAK.GPVGDK.HVSTRVMGTYGYCAPE
Retrocopy AQGAARGLEHLHDAARPPVIYRDFKASNILLDSSFQARLSDFGLAKVGPVGDKTHVSTRVMGTYGYCAPE

Parental  YAMTGQLTVKSDVYSFGVVLLELITGRRAIDSTRPHGEQNLVSWARPLFNDRRKLPKMADPRLEGRYPMR
          YA.TG.LT..SDVYSFGVV.LE.ITGRRAID..RPH.EQNLV.WA.P.F.D......MADP.L.G.YP..
Retrocopy YALTGKLTTCSDVYSFGVVFLEIITGRRAIDMARPHDEQNLVQWAAPRFKDKKLFADMADPLLRGAYPTK

Parental  GLYQALAVASMCIQSEAASRPLIADVVTALSYL
          GLYQALA.A.MC.Q..A..RP.I.DVVTAL.YL
Retrocopy GLYQALAIAAMCLQEDATMRPAISDVVTALEYL

Legend:

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

Expression

RNA-Seq

Oryza longistaminata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_6 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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
Oryza longistaminata	KN539056.1_FG008	1 retrocopy	retro_olon_6 ,