RetrogeneDB ID: retro_oind_41

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02039389.1:4806..6105(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA038668
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA014839
• Aliases: None
• Description: None

Sequence

>retro_oind_41
ATGGTGATCAATGCGTTGAACGCCAACGTAAAAGTGTTTATGGCGGACTTCGAAGACTCACTGGCGCCAAGCTGGGACAA
AGTCATCGACGGCCAAATCAATCTGCACGATGCGGTTAACGGCACCATCTCCTACACCAATGAAGCCGGCAAGATCTACC
AGCTGAAACCGAACCCGGCGGTATTGATCGCACGCGTACGCGGTCTGCATCTGCCGGAGAAGCACGTGCTGTGGCGTGAT
GAGGCCATTCCCGGCGGCCTGTTCGATTTCGCGCTGTACTTCTACCACAACTATCGCCAGCTGCTGGCCAAGGGCAGCGG
CCCGTATTTCTACCTGCCGAAAACCCAGTCCTGGGAGGAAGCTGCCTGGTGGAGCGATGTCTTCAGCTTTACCGAGGATC
GTTTCGATCTGCCGCGCGGCACCATCAAAGCGACCGTGCTGATCGAAACTCTGCCGGCGGTGTTCCAGATGGACGAGATC
CTGTATCACCTGCGCGATCACATCGTCGGTCTGAACTGCGGCCGCTGGGATTACATCTTCAGCTACATCAAAACGCTGAA
GAACCACGGCGATCGCGTGCTGCCGGATCGTCAGTCGGTGACCATGGAAAAACCTTTCCTCAGCGCCTATTCGCGCCTGT
TGATCAAAACCTGTCATAAGCGCGGCGCGTTCGCCATGGGCGGCATGGCGGCGTTTATCCCGAGCAAAGACGCCGAGAAA
AATGCCTGGGTGCTGAACAAGGTGCGGGCGGACAAAGAGCTGGAAGCCAACAATGGGCACGACGGCACCTGGGTGGCGCA
CCCGGGCTTGGCGGACACGGTGATGGAGGTGTTCGGCAACGCATTGGGCGATCGCCAGAACCAGCTGGACGTGCTGCGTG
AGCAGGATGCGCCGATCAGCGCCGCGCAACTGCTGGAACCGTGCGACGGCGAACGCACCGAAGCGGGGATGCGCGCCAAT
ATCCGCGTGGCGGTGCAGTACATCGAAGCCTGGATCTCCGGCAACGGCTGCGTGCCTATCTATGGGTTGATGGAAGATGC
CGCGACGGCGGAGATCTCCCGTACCTCTATCTGGCAGTGGATCCACCATGAGAAGAGCCTGAACGACGGGCGCCCGGTCA
CCAAGGCGCTGTTCCGCCAGATGTTGCAAGAAGAGATGTTGGTGGTGCGTGAAGAAGTAGGGGAAGCGCGCTTTAACGCC
GGCCGGTTCGAAGAGGCGGCGCGCCTGATGGAGCGCATCACCACGCAAGATGAATTAATCGACTTCCTGACGTTGCCCGG
CTATGCGCTGCTGGCCTGA

Alignment

ORF - retro_oind_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.82 %
• Parental protein coverage: 78.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVINALNSGAKVFMADFEDALSPTWENLMRGQVNLRDAVAGTITYRDAARGREYRLGDRPATLFVRPRGW
          MVINALN...KVFMADFED.L.P.W.....GQ.NL.DAV.GTI.Y...A.G..Y.L...PA.L..R.RG.
Retrocopy MVINALNANVKVFMADFEDSLAPSWDKVIDGQINLHDAVNGTISYTNEA-GKIYQLKPNPAVLIARVRGL

Parental  HLPEAHVLVDGEPAIGCLVDFGLYFFHSHAAFRSGQGADFGPFFYLPKMEHSREARIWKGVFERAEKEAG
          HLPE.HVL...E...G.L.DF.LYF.H.....R.......GP.FYLPK.....EA..W..VF...E....
Retrocopy HLPEKHVLWRDEAIPGGLFDFALYFYHN---YRQLLAKGSGPYFYLPKTQSWEEAAWWSDVFSFTEDRFD

Parental  IGRGSIRATVLVETLPAVFQMEEILHELRDHSAGLNCGRWDYIFSYVKTFRARPDRLLPDRALVGMAQHF
          ..RG.I.ATVL.ETLPAVFQM.EIL..LRDH..GLNCGRWDYIFSY.KT.....DR.LPDR..V.M...F
Retrocopy LPRGTIKATVLIETLPAVFQMDEILYHLRDHIVGLNCGRWDYIFSYIKTLKNHGDRVLPDRQSVTMEKPF

Parental  MRSYSHLLIQTCHRRGVHAMGGMAAQIPIKDDAAANEAALELVRKDKLREVRAGHDGTWAAHPGLIPAIR
          ...YS.LLI.TCH.RG..AMGGMAA.IP.K.DA..N...L..VR.DK..E...GHDGTW.AHPGL.....
Retrocopy LSAYSRLLIKTCHKRGAFAMGGMAAFIPSK-DAEKNAWVLNKVRADKELEANNGHDGTWVAHPGLADTVM

Parental  EVFEGHLGGRPNQIDAAAGDAARAGVAVTEEDLLQPPRGARTVEGLRHNTRVGVQYVAAWLSGSGSVPLY
          EVF...LG.R.NQ.D......A....A.....LL.P..G.RT..G.R.N.RV.VQY..AW.SG.G.VP.Y
Retrocopy EVFGNALGDRQNQLDVLREQDAPISAA----QLLEPCDGERTEAGMRANIRVAVQYIEAWISGNGCVPIY

Parental  NLMEDAATAEISRVQNWQWLRHGAVLDAGGVEVRATPELLARVVEVEMARVEAEVGAERFRRGRYAEAGR
          .LMEDAATAEISR...WQW..H...L..G.....A...L.......EM..V..EVG..RF..GR..EA.R
Retrocopy GLMEDAATAEISRTSIWQWIHHEKSLNDGRPVTKA---LFRQMLQEEMLVVREEVGEARFNAGRFEEAAR

Parental  IFSRQCTAPELDDFLTLDAYNLI
          ...R..T..EL.DFLTL..Y.L.
Retrocopy LMERITTQDELIDFLTLPGYALL

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_41 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 sativa indica	BGIOSGA014839	1 retrocopy	retro_oind_41 ,