RetrogeneDB ID: retro_oind_54

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 11:21906096..21907296(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA035680
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA036000
• Aliases: None
• Description: None

Sequence

>retro_oind_54
ATGGATCGTCCCAACCTCGCCGTGGCCGTGGTGGGGCTACTGGCGGTGGTGGCGGCGACGCTGCCGGCGCCGTCATGGCA
GTTCTTCGACCTATTCCTCCCCGCCGGCCCCAGCCACCGCTCCTCCGGCGGAGGGTTTGGCAAGTGGGTGCTGATGAACC
ACGAGGAGTACGTCGAGAAGAAGTCGCTGTACGCCATGAAGGCCGCCGGCGACATCGGCGGGAAGACCATCGACGCGAGC
CTCTCGGCGGCGGAGGAGGCCAAGGTGACGTGGGTGGTTGACCCCAAGGGGACGCCGGGCGACACCACCTTCACCACCAT
CGCGGCGGCGCTCGAGAAGGTCCCCGAGGGGAACACCAAGCGCGTCATCCTCGACCTCAAGCCCGGCGCCGAGTTCCGGG
AGAAGCTCCTCCTCAACATCACTAAGCCCTACATCACCTTCAAGTCCGACCCCGCCAACCCGGCGGTGATCGCCTGGAAC
GACATGGCTGCCACCAGGGGCAAGGACGGCAAGCCCGTCGGCACCGTCGGGAGCACCACCGTCGCCGTCGAGTCCGACTA
CTTCATGGCCTACGGCGTCGTCTTCAAGAACGACGCGCCGCTGGCCAAGCCGGGTGCCGAGGGTGGCCAGGCGGTGGCGC
TCCGCCTGTTCGGCACCAAGGCAGCCATCTACAACTGCACCATCGACGGCGGGCAGGACACCCTATACGATCACAAGGGA
CTCCACTACATCAAGGATAGCCTCATCATGGGCAGCGTCGACTTCATCTTTGGATTCGGGAGATCACTCTACGAGGGCTG
CACCATCGTCTCCGTCACCAAGGAGGTGTCCGTGCTGACGGCGCAGCAGAGGACCAAGACCATCGAGGGCGCCATAGAAA
GTGGCTTCTCCTTCAAGAACTGCAGCATCAAAGGACAAGGGCAGATCTACCTCGGCCGGGCATGGGGGGATTCGTCGCGG
GTGGTGTACTCCTACACGGACATGTCCAAGGAGGTGGTGCCGATAGGGTGGGATGGCTGGAACATCGCCAAGCCGGAGAG
CAGCGGGATCTACTACGGCGAGTTCAAGTGCACCGGCCCCGGCTCCGACGCCAAGAAGAGGGTGGGTTGGGCGCTTGACC
TCACCGCGGATCAGGCCAAGCCCTTCATCGGCACGCACTACATCTATGGCGACTCATGGATCCTCCCGCCACCAGAGTAA

Alignment

ORF - retro_oind_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.04 %
• Parental protein coverage: 83.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSFSDFVTQNVQHYV----LSEQKYAGKV--KALDAELSAAEAGAARYVVSGD---GKGKFRTITDAIKA
          G.F...V..N...YV....L...K.AG....K..DA.LSAAE......VV......G...F.TI..A...
Retrocopy GGFGKWVLMNHEEYVEKKSLYAMKAAGDIGGKTIDASLSAAEEAKVTWVVDPKGTPGDTTFTTIAAALEK

Parental  VPEYNKKRVILDIRPGT-YKEKLLIPFTKPFITFVGNPRSPPTIMWDDRAATHGKDGQPMGTMLSATVAV
          VPE.N.KRVILD..PG....EKLL...TKP.ITF...P..P..I.W.D.AAT.GKDG.P.GT..S.TVAV
Retrocopy VPEGNTKRVILDLKPGAEFREKLLLNITKPYITFKSDPANPAVIAWNDMAATRGKDGKPVGTVGSTTVAV

Parental  EADYFMASGIIFKNHAPMAAPGAHGGQAVALRVFGSKVAMYNCTIDGGQDTLYDHKGLHYFKNCLIRGSV
          E.DYFMA.G..FKN.AP.A.PGA.GGQAVALR.FG.K.A.YNCTIDGGQDTLYDHKGLHY.K..LI.GSV
Retrocopy ESDYFMAYGVVFKNDAPLAKPGAEGGQAVALRLFGTKAAIYNCTIDGGQDTLYDHKGLHYIKDSLIMGSV

Parental  DFIFGFGRSLYADCTIESVTKEVAVVTAQQRSKNIAEAIDTGFSFLRCKISGIGQIYLGRAWGDSSRVVY
          DFIFGFGRSLY..CTI.SVTKEV.V.TAQQR.K.I..AI..GFSF..C.I.G.GQIYLGRAWGDSSRVVY
Retrocopy DFIFGFGRSLYEGCTIVSVTKEVSVLTAQQRTKTIEGAIESGFSFKNCSIKGQGQIYLGRAWGDSSRVVY

Parental  SYTTMGKEVVPIGWDGWEVQKPEHSGIYYGEYKCSGPGALPSKRIGWSLVLSDIQAKPFTGSHFVYGDSW
          SYT.M.KEVVPIGWDGW...KPE.SGIYYGE.KC.GPG....KR.GW.L.L...QAKPF.G.H..YGDSW
Retrocopy SYTDMSKEVVPIGWDGWNIAKPESSGIYYGEFKCTGPGSDAKKRVGWALDLTADQAKPFIGTHYIYGDSW

Parental  ILPPPK
          ILPPP.
Retrocopy ILPPPE

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_54 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA036000	1 retrocopy	retro_oind_54 ,
Zea mays	GRMZM2G382557	1 retrocopy	retro_zmay_21,