RetrogeneDB ID: retro_oind_48

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 7:21190736..21191192(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA025984
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA027748
• Aliases: None
• Description: None

Sequence

>retro_oind_48
ATGGGCCGCATGCACAGCAGCGGGAAGGGGATGTCCTGCTCGGTGCTCCCCTACAGGCGCGCCGCTCCCGCCTGGGTCAA
GACGTCCGCGTCGGAGGTGGAGGAGATGATCGTGCGCGCCGCCAAGAAGGGCCAGCTGCCGTCGCAGATCGGGGCGATCC
TCCGCGACGCCCACGCCGTCCCGCTCGCCCAGGGCGTCACCGGCGGCAAGATCCTCCGCGTGCTCAAGTCCCGCGGCCTC
GCGCCCGAGGTGCCCGAGGACCTCTACTTCCTCATCAAGAAGGCCGTCGCGATGAGGAAGCACCTCGAGAGGAACAGGAA
GGACAAGGACACCAAGTTCCGCCTCATCCTCGTCGAGAGCAGGGTGCACCGCCTCACCCGCTACTACCGCCTCGCCAAGA
AGATCCCCGCCTTCTTCAAGTACGACTCCACCACCGCGAGCACTCTCGTGGCCTGA

Alignment

ORF - retro_oind_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRMHSRGKGISSSALPYKRTPPSWLKTAASDVEEMIMKAAKKGQMPSQIGVVLRDQHGIPLVKSVTGSK
          MGRMHS.GKG.S.S.LPY.R..P.W.KT.AS.VEEMI..AAKKGQ.PSQIG..LRD.H..PL...VTG.K
Retrocopy MGRMHSSGKGMSCSVLPYRRAAPAWVKTSASEVEEMIVRAAKKGQLPSQIGAILRDAHAVPLAQGVTGGK

Parental  ILRILKAHGLAPEIPEDLYFLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKRTKKLPPTWK
          ILR.LK..GLAPE.PEDLYFLIKKAVA.RKHLERNRKDKD.KFRLILVESR.HRL.RYY...KK.P...K
Retrocopy ILRVLKSRGLAPEVPEDLYFLIKKAVAMRKHLERNRKDKDTKFRLILVESRVHRLTRYYRLAKKIPAFFK

Parental  YESTTASTLVA
          Y.STTASTLVA
Retrocopy YDSTTASTLVA

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_48 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027748	1 retrocopy	retro_oind_48 ,
Leersia perrieri	LPERR08G01520	1 retrocopy	retro_lper_15,
Oryza sativa japonica	OS08G0117300	1 retrocopy	retro_osat_33,
Sorghum bicolor	Sb07g001620	1 retrocopy	retro_sbic_47,