RetrogeneDB ID: retro_oind_11

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: CH401014.1:241..670(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA040390
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA004458
• Aliases: None
• Description: None

Sequence

>retro_oind_11
ATGTCCACTTTCAGCGCAAAGCCCGCTGAGGTCGTGCACGAGTGGTTTGTGATTGACGCGACCGACAAGGTCCTCGGACG
AGTAGCCAGCGAAGTTGCTCTCCGTCTGCGCGGCAAACACAAGGCCATTTACACGCCTCACGTCGATACCGGCGATTTCA
TCGTCATCATCAACGCCTCCAAGCTCAAGGTCACCGGCACCAAGTCCCTGGACAAGGTGTACTACCGCCACTCCGGCTAT
CCCGGTGGCATCACGGCGACGAACTTCCGCGACCTGCAGGCCAAGCACCCCGGCCGCGCACTCGAGAAGGCCGTCAAGGG
CATGCTGCCCAAGGGCCCCCTGGGCTACGCCATGATCAAGAAGCTCAAGGTCTACGGCGGCGCGGAACATCCGCACACCG
CTCAGCAGCCCAAGGCGCTGGAAATCTAA

Alignment

ORF - retro_oind_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.47 %
• Parental protein coverage: 54.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WYVVDATDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVVNAEKVAVSGKKRSQKLYRRHSGRPGGM
          W.V.DATDK.LGR.AS..A...RGK..A.YTP.VD.G.F.V..NA.K..V.G.K...K.Y.RHSG.PGG.
Retrocopy WFVIDATDKVLGRVASEVALRLRGKHKAIYTPHVDTGDFIVIINASKLKVTGTKSLDKVYYRHSGYPGGI

Parental  KEETFDQLQKRIPERIIEHAVRGMLPKGRLGRRLFTHLKVYKGAEHPHEAQKPVPLPI
          ....F..LQ...P.R..E.AV.GMLPKG.LG......LKVY.GAEHPH.AQ.P..L.I
Retrocopy TATNFRDLQAKHPGRALEKAVKGMLPKGPLGYAMIKKLKVYGGAEHPHTAQQPKALEI

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_11 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	BGIOSGA004458	1 retrocopy	retro_oind_11 ,