RetrogeneDB ID: retro_oind_35

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02041357.1:3280..4234(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039139
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA009239
• Aliases: None
• Description: None

Sequence

>retro_oind_35
ATGGCGACCACCATGCGTGCCGTGGAAATCGCGGGCTCCGGCGGCCCGGAAGTACTGCGCCTCGCCGAGCGGCCCGTGCC
GCGGCCGGGCGCAGGCGAGCTGCTGATCCGCGTCGCGGCCAGCGGCATCAACCGGCCCGACGTGCTCCAGCGCAAGGGGC
ACTATGCGCCCCCGCCGGGCGCTTCCGACCTGCCCGGGCTCGAAGTGGCGGGCACCATCACGGAAGGCGACGCGTCGGCG
ATGGCCGCGGCTGGCCTGAAGGCGGGCGACCGCGTGTGCGCGCTGGTCGCGGGCGGCGGCTATGCCGAATGGTGCGTCGC
ACCCGTCGCGCAATGCCTGCCCGTGCCGGAGGGCTGGAGCGACGTGGAGGCGGCCTCGCTGCCCGAGACCTTCTTCACGG
TGTGGAGCAACGTGTTCGACCGCGGCCGCCTCGCGGCTGGCGAAACCCTGCTGGTGCAGGGCGGCAGCAGCGGCATCGGC
GTGACGGCCATCCAGCTCGGCCGCGCCTTCGGCGCCACGGTGATCGTGACGGCGGGCTCGGACGAGAAGTGCCGCACCTG
CCTGGAGCTCGGCGCGCACCATGCCATCAACTACAAGACCCAGGACTTCGTGGCCGAGGCCCGGCGCATCACCGATGGCC
GCGGCGTGGACGTGGTACTCGACATGGTGGCGGGCGACTACGTGGCGCGCGAGGTCGAGTGCCTGGCCGAGGATGGCCGC
CTGGTCATCATCGCCGTGCAGGGCGGGGTGCAGTCCTCCTTCGATGCAGGGCTGGTGCTGCGCCGCCGCCTCACGGTGAC
GGGCTCGACGCTGCGGCCCCGTTCCGTCGCGTCAAGGGCGCCATCGCTGCCGCCCTGCGCGAGCGGGTGTGGCCGCTGCT
GGCGGCCCGCACCGTGCGGCCCGTGGTGCACAGCACCTTCCCGGCGGCCGAGGCGTCGCGGGCCCATGCGCTGA

Alignment

ORF - retro_oind_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.08 %
• Parental protein coverage: 58.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDQVCALLSGGGYAEKVVVPAGQLLPVPEGVSLTDAAGLPEVACTVWSTVFVTSHLSPSESFLIHGGSSG
          GD.VCAL..GGGYAE..V.P..Q.LPVPEG.S...AA.LPE...TVWS.VF....L...E..L..GGSSG
Retrocopy GDRVCALVAGGGYAEWCVAPVAQCLPVPEGWSDVEAASLPETFFTVWSNVFDRGRLAAGETLLVQGGSSG

Parental  IGTFAIQIAKHLGIKVFVTAGSEEKLAACKGLGADVCINYKTEDFVARVKEETNGKGVDVILDNIGGLYL
          IG..AIQ.....G..V.VTAGS.EK...C..LGA...INYKT.DFVA.....T.G.GVDV.LD...G.Y.
Retrocopy IGVTAIQLGRAFGATVIVTAGSDEKCRTCLELGAHHAINYKTQDFVAEARRITDGRGVDVVLDMVAGDYV

Parental  QRNLNSLAVDGRLFIIGFQGGAVTEVNLQPMLARRLTIQAAGLRNRSLDNKA
          .R....LA.DGRL.II..QGG..........L.RRLT.....LR.RS....A
Retrocopy AREVECLAEDGRLVIIAVQGGVQSSFDAGLVLRRRLTVTGSTLRPRSVASRA

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_35 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	BGIOSGA009239	1 retrocopy	retro_oind_35 ,
Triticum aestivum	Traes_6DL_237C26703	1 retrocopy	retro_taes_181,