RetrogeneDB ID: retro_olon_8

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN541235.1:1189..2767(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN541235.1_FG001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN539459.1_FG006
• Aliases: None
• Description: None

Sequence

>retro_olon_8
ATGGCACCACCTTCGCACTGCCACGCCACGAATGGCGGTGGTGCCCCACAGCACAATGGCGCCAACGCCGTTGACGCGCC
GGTGACACGAAGCGCGCGACTGCTCGACGCCGAGGAGTTCCGGCGTCACGGTCACCTGGTTGTCGACTTTATCGCCGACT
ACTATGCCGGCTTGGGGGAATACCCCGTGCACCCTAGTGTGAGCCCTGGCTTCCTTCGCCACCACCTCCCGGTGGAGCCG
CCGTCCCGCCGGGAACCCGACGCGTTCGACGCGGCGCTGCAGGATGTCCGTAACGTCATCCTGCCGGGGTTGACGCACTG
GCAGAGCCCCCGCCACTTCGCGCACTTCCCGGCGTCGAGCAGCACCGTCGGTGCCCTCGGCGAGGCGCTCGCCGCCGGTA
TCAACGTCGTTCCTTTCACGTGGGCGTCCTCGCCGGCAGCCACCGAGCTTGAGATGGTTGTCGTGGACTGGCTCGGCAAG
GCGCTTCACCTGCCGGAGAGGATGCTGTTCGCCGGAGGCGGAGGCGGCACCATCCTCGGGACCACGTGCGAGGCGATCCT
CAGCGCCCTCGTCGCCGCGAGGGACCGCAAGCTCGCGGTGATCGGAGAGGATAGGATCGGCGATCTCGTCGTCTACTGCT
CGGACCAGACCCACTTCGCGTTCTGCAAGGCGGCGCGTATCGCCGGCATCCGGCGTGAGCATTGCCGCGAGATACCGACG
TACCGCGACGACACGTTCGCGCTCTCGCCGACCGAGCTGCAGGCCGCCATGCAGCGCGACGTCGACGCCGGCCTGGTCCC
CCTGTTCCTGTGCGCCACGATCGGGACCACCCAGACGACCGCCGTAGACCCCGTCGGCGAGCTCTGCGCCGTCGCGGCGC
TGCACGGCGCCTGGGTGCACGTCGACGCGGCGTACGCAGGGTCGGCGCTGGTGTGCCCGGAGTTCCGCGGCGTGATCGCC
GGCGTCGAGGCCGCGGACTCGTTCAGCATGAACGCCCACAAGTGGTTGCTGGCGAACAACGACTGCTGCGTGATGTGGGT
GAGGACGCCGTCGGCGCTGGTGGCGGCGCTGGGCACGGAGCAGGACTACATCCTCAAGGACGCTGCGGCGGAGGGCGTCG
TCGACTACAAGGACTGGGGCATGACGCTGACGCGGCGGTTCCGCGCGCTCAAGGTCTGGCTCGTGCTCCGCTGCTACGGC
GTGGAGGGCCTGCGCGAGCACGTCCGGTCCCACGTCCGCATGGCCGCCGCGTTCGAGGGCATGGTCAGAGCAGACGCGAG
GTTCGAGGTGGTGACGCCGAGGCGATTCGCGCTGGTGTGCTTCCGGCTCCGGTCACCGAAGAACTACAGGTTCGCCGGCG
GCGAGAAGTCGGCCAACGAGCTCAACAGGCGTCTCCTCGAGGAGGTGAACGCGGCCAGCTCGGGACCGTACATGAGCTCC
GGTAAGGTCGGCGGCGTGTACATGCTCAGGTGCGCCGTCGGCAGCACGCTCACCGAGGAGCGCCACGTCCGGGAAGCGTG
GAAGGCTGTCCAGGATCGGGCTACGTCCATCCTTCGTAAAATGGAGACTATTATGTAG

Alignment

ORF - retro_olon_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.81 %
• Parental protein coverage: 64.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FNWITSPAATELEVIVLDWFAKMLQLPSQFLSTALGGGVIQGTASEAVLVALLAARDRALKKHGKHSLEK
          F.W..SPAATELE..V.DW..K.L.LP...L....GGG.I.GT..EA.L.AL.AARDR.L...G......
Retrocopy FTWASSPAATELEMVVVDWLGKALHLPERMLFAGGGGGTILGTTCEAILSALVAARDRKLAVIGEDRIGD

Parental  LVVYASDQTHSALQKACQIAGIFSENVRVVIAHCNTNYAVAPEAVSEALSIDLSSGLIPFFICATVGTTS
          LVVY.SDQTH.A..KA..IAGI..E..R..........A..P.....A...D...GL.P.F.CAT.GTT.
Retrocopy LVVYCSDQTHFAFCKAARIAGIRREHCREIPTYRDDTFALSPTELQAAMQRDVDAGLVPLFLCATIGTTQ

Parental  SSAVDPLPELGQIAKSNDMWFHIDAAYAGSACICPEYRHHLNGVEEADSFNMNAHKWFLTNFDCSLLWVK
          ..AVDP..EL...A.....W.H.DAAYAGSA..CPE.R....GVE.ADSF.MNAHKW.L.N.DC...WV.
Retrocopy TTAVDPVGELCAVAALHGAWVHVDAAYAGSALVCPEFRGVIAGVEAADSFSMNAHKWLLANNDCCVMWVR

Parental  DRSFLIQSLSTNPEFLKNKASQANSVVDFKDWQIPLGRRFRSLKLWMVLRLYGVDNLQSYIRKHIHLAEH
          ..S.L...L.T........A..A..VVD.KDW...L.RRFR.LK.W.VLR.YGV..L....R.H...A..
Retrocopy TPSALVAALGTEQDYILKDAA-AEGVVDYKDWGMTLTRRFRALKVWLVLRCYGVEGLREHVRSHVRMAAA

Parental  FEQLLLSDSRFEVVTPRTFSLVCFRLVPP
          FE.....D.RFEVVTPR.F.LVCFRL..P
Retrocopy FEGMVRADARFEVVTPRRFALVCFRLRSP

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_8 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539459.1_FG006	1 retrocopy	retro_olon_8 ,
Hordeum vulgare	MLOC_77509	1 retrocopy	retro_hvul_50,