RetrogeneDB ID: retro_oind_59

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: CH399561.1:3949..5014(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA038942
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA013198
• Aliases: None
• Description: None

Sequence

>retro_oind_59
ATGGCTATTGATGAGAACAAGCAAAAGGCGTTAGCTGCGGCACTGGGCCAGATTGAGAAACAGTTCGGCAAAGGCTCCAT
CATGCGCCTGGGTGAAGACCGCTCCATGGACGTGGAAACCATCTCCACCGGCTCACTGTCACTCGATATCGCTCTGGGCG
CCGGCGGCCTGCCGATGGGCCGCATCGTCGAAATCTACGGCCCGGAATCGTCCGGTAAAACCACCCTGACGCTGCAGGTG
ATCGCCGCCGCGCAGCGCGAAGGCAAAACCTGTGCGTTCATCGATGCCGAGCACGCGCTGGATCCTATCTATGCGAAAAA
GCTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGAGCAGGCGCTGGAAATCTGTGATGCGCTGA
CCCGCTCCGGCGCGGTTGACGTCATCATCGTCGACTCCGTGGCGGCGCTGACGCCGAAGGCGGAAATCGAAGGTGAAATC
GGCGATTCGCACATGGGGTTGGCGGCGCGCATGATGAGCCAGGCGATGCGTAAGCTGGCCGGCAACCTGAAAAATGCCAA
TACCCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTTCGGCAACCCGGAAACCACTACCGGTGGTA
ACGCTCTGAAGTTCTATGCTTCGGTGCGTCTGGATATCCGTCGTATCGGCGCCATCAAAGAGGGCGACGAAGTGGTGGGC
AGCGAAACCCGCGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTCAAACAGGCTGAGTTCCAAATCATGTACGGTGA
AGGCATCAACAGCCGTGGTGAACTGGTCGATCTGGGCGTGAAGCACAAGATGATCGAAAAAGCCGGCGCTTGGTACAGCT
ATAACGGCGAGAAGATCGGTCAGGGCAAGGCGAACGCCTGTAACTTCCTGAAAGAAAACCCGGCTATCGCCGCCGAGCTG
GATAAGAAACTGCGCGACCTGCTGCTGCACAGCGGCGGTGAGCTGGTGGCTGCCTCCGGTGACGACTTCGAAGATGACGA
AGCGGAAACCAGCGAGCAGTTTTAA

Alignment

ORF - retro_oind_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.04 %
• Parental protein coverage: 73.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKALDAAMNDINSSFGKGSVTRLGSAGGAFVETFPSGCLTLDFALG-GGLPKGRVVEVYGPESSGKTTLA
          QKAL.AA...I...FGKGS..RLG......VET...G.L.LD.ALG.GGLP.GR.VE.YGPESSGKTTL.
Retrocopy QKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLT

Parental  LHAIAEVQKLGGNAMLVDAEHAFDPAYSKALGVDIENLIVCQPDNGEMALEIADRMCRSGAIDLICIDSV
          L..IA..Q..G......DAEHA.DP.Y.K.LGVDI.NL...QPD.GE.ALEI.D...RSGA.D.I..DSV
Retrocopy LQVIAAAQREGKTCAFIDAEHALDPIYAKKLGVDIDNLLCSQPDTGEQALEICDALTRSGAVDVIIVDSV

Parental  SALTPRAEIEGEIGMQQMGLQARLMSQALRKMSGNASKAGCTLMFLNQIRYKIGVFYGNPEVTSGGIALK
          .ALTP.AEIEGEIG...MGL.AR.MSQA.RK..GN...A...L.F.NQIR.KIGV..GNPE.T.GG.ALK
Retrocopy AALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKNANTLLIFINQIRMKIGVMFGNPETTTGGNALK

Parental  FFASVRLEIRPIGKIKSAKGDEDVGVKVRVRVQKSKVSRPYKQAEFEIIFGEGVSKLGCVLDCAELMEVV
          F.ASVRL.IR.IG.IK...GDE.VG...RV.V.K.K...P.KQAEF.I..GEG....G...D........
Retrocopy FYASVRLDIRRIGAIK--EGDEVVGSETRVKVVKNKIAAPFKQAEFQIMYGEGINSRGELVDLGVKHKMI

Parental  AKKGSWYSYKEMRLGQGREKALQYLRESPTICDEIEKAVRAMI
          .K.G.WYSY.....GQG...A...L.E.P.I..E..K..R...
Retrocopy EKAGAWYSYNGEKIGQGKANACNFLKENPAIAAELDKKLRDLL

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_59 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	BGIOSGA013198	1 retrocopy	retro_oind_59 ,