RetrogeneDB ID: retro_oind_3

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02038326.1:1634..2663(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA038465
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA035012
• Aliases: None
• Description: None

Sequence

>retro_oind_3
ATGCAAGCGCTTAACACCACCAGTTTGACCCTGCGGGACAACCGCCTTTGGATCCTCGATCAGCAAGCCCTGCCACAGGA
AAAGCGGTGGCGCGCCTGCGACAGCGTGGAGGAGTTGGTCGGGCACATTCACAGCCTGCGGGTGCGCGGCGCGCCGCTGA
TCGGGCTGTCCGCCAGCCTGCTGTTGGCGCTGCTGGCGGAACGCGGTGTGCCGCGCGCCGAGCTGGAACAGGCGCTGCAC
ACGCTGCGCGCCGCCCGCCCGACGGCGGTTAACCTGATGAACAATCTGGATCGCATGAAGCTGGCGCTGGCGGAGCCTGA
CTGGGTGCCGGCGATGGCGAACGAAGCGCTGCGGCTGGTGGAGGAAGATCGCCGGCTGTGCGATCGCATCGCCGATCACG
GCGCTGGTCTGATCAAGCCCGGCAGCCGCCTGCTGACCCACTGCAATACCGGCGGGTTGGCCACCGCCGGCGTCGGCACC
GCCATCGGCGTGCTGCTGCGCGCCCACCAGCAGGGCAAAGTGCAACAGGTATGGGTTGATGAAACCCGGCCGCTGCTGCA
GGGCGGCCGTCTGACCGCCTGGGAACTGGGCGAGCTGGGCATTCCCTATCGTCTGATCTGCGATTCGATGGCCGCCAGCC
TGATGGCGCAGGGCCAGGTCGATGCGGTGTGGGTCGGCGCGGATCGCATCGCCGCCAACGGCGACGTCGCCAACAAGATT
GGCACCTACAGCCTGGCGGTGCTGGCGCACTACCATGGCATTCCATTCTATGTGGCTGCCCCGCATACCACCCACGATCC
GCACTGTCCGGACGGCGCCGCCATCCCGATCGAGCAACGCGCGGCGGCCGAAGTCACCGGCGTTTCAGGCAGTTTCGGCG
CCTGCCAGTGGGCGCCGGCCGATGCGCCGGTCTGCAATCCGGCGTTCGACGTCACGCCGGCCAAGCTTATCAGCGGGTGG
GTGTTCGACAGCGGCGTGATCACGCCGCAGCAGGTTGAAGCGGGGATTTTCCAGCGGGCGCTGGGTTAA

Alignment

ORF - retro_oind_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.16 %
• Parental protein coverage: 50.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLTHCNTGSLATAGYGTALGVIRALHSGGILEKAFCTETRPFNQGSRLTAFELVHDKVPATLIADSAAAA
          .LTHCNTG.LATAG.GTA.GV....H..G........ETRP..QG.RLTA.EL.....P..LI.DS.AA.
Retrocopy LLTHCNTGGLATAGVGTAIGVLLRAHQQGKVQQVWVDETRPLLQGGRLTAWELGELGIPYRLICDSMAAS

Parental  LMKSGCIQAVIVGADRIAANGDTANKIGTYNLAISAKHHGVQFYVAAPITSIDLSLPSGEQIVIEERSPN
          LM..G...AV.VGADRIAANGD.ANKIGTY.LA..A..HG..FYVAAP.T..D...P.G..I.IE.R...
Retrocopy LMAQGQVDAVWVGADRIAANGDVANKIGTYSLAVLAHYHGIPFYVAAPHTTHDPHCPDGAAIPIEQRAAA

Parental  ELLNSEGGLGK-QVAASGISVWNPAFDVTPANLITAIITEKGVITKSDAD
          E.....G..G..Q.A.....V.NPAFDVTPA.LI.......GVIT.....
Retrocopy EVTGVSGSFGACQWAPADAPVCNPAFDVTPAKLISGWVFDSGVITPQQVE

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_3 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	BGIOSGA035012	1 retrocopy	retro_oind_3 ,