RetrogeneDB ID: retro_olon_12

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN539003.1:75682..76510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN539003.1_FG015
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN540387.1_FG001
• Aliases: None
• Description: None

Sequence

>retro_olon_12
ATGGGCAGGGAGGAGTTCCGCGCCACGTTCGCCGGGTCCCACGCCAACGACCTCCGCCGCGACGGCCTCGCCGCGCCGCC
GCTCCCGGGGTTCATGTACGAGGGCGTCCGCGACCTCCCCCGCGCCGTCGACTGGCGCCGCAAGGGCGCGGTCACCGGCG
TCAAGGACCAGGGCAAGTGCGGCAGCTGCTGGGCGTTCTCCACGGTGGTGTCCGTGGAGGGCATCAACGCGATCCGGACG
GGGCGTCTGGTGTCGCTGTCGGAGCAGGAGCTGATCGACTGCGACACGGCGGACAACAGCGGCTGCCAGGGCGGGCTCAT
GGAGAACGCGTTCGAGTACATCAAGCACAGCGGCGGCATCACCACCGAGTCCGCCTACCCGTACCGCGCCGCCAACGGAA
CGTGCGACGCCGTCCGCGCGCGGCGCGCGCCGCTGGTGGTGATCGACGGGCACCAGAACGTGCCGGCCAACAGCGAGGCC
GCGCTCGCCAAGGCCGTCGCCAACCAGCCCGTCTCCGTCGCCATCGACGCCGGCGACCAGTCCTTCCAGTTCTACTCCGA
CGGCGTCTTCACCGGCGACTGCGGCACCGACCTCGACCACGGCGTCGCGGTGGTCGGCTACGGCGAGACCAACGACGGCA
CGGAGTACTGGATCGTCAAGAACTCGTGGGGCACAGCCTGGGGCGAGGGCGGCTACATCCGGATGCAGCGCGACTCCGGC
TACGACGGCGGCCTCTGCGGCATCGCCATGGAAGCCTCCTACCCCGTCAAGTTCTCGCCAAATCGTGTCACGCCAAGGCG
CGCCCTTGGCGCCAAGGAAACCCAGTGA

Alignment

ORF - retro_olon_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.92 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CWAFSAVAAVEGVNKIKTGRLVTLSEQELVDCDTGDNQGCDGGLMDYAFQFIKRNGGITTESNYPYRAEQ
          CWAFS.V..VEG.N.I.TGRLV.LSEQEL.DCDT.DN.GC.GGLM..AF..IK..GGITTES.YPYRA..
Retrocopy CWAFSTVVSVEGINAIRTGRLVSLSEQELIDCDTADNSGCQGGLMENAFEYIKHSGGITTESAYPYRAAN

Parental  GRCNKAKASSHD-VTIDGYEDVPANDESALQKAVANQPVAVAIEASGQDFQFYSEGVFTGECGTDLDHGV
          G.C....A.....V.IDG...VPAN.E.AL.KAVANQPV.VAI.A..Q.FQFYS.GVFTG.CGTDLDHGV
Retrocopy GTCDAVRARRAPLVVIDGHQNVPANSEAALAKAVANQPVSVAIDAGDQSFQFYSDGVFTGDCGTDLDHGV

Parental  AAVGYGITRDGTKYWIVKNSWGEDWGERGYIRMQRGVSSDSNGLCGIAMEASYPVK
          A.VGYG.T.DGT.YWIVKNSWG..WGE.GYIRMQR....D..GLCGIAMEASYPVK
Retrocopy AVVGYGETNDGTEYWIVKNSWGTAWGEGGYIRMQRDSGYD-GGLCGIAMEASYPVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza longistaminata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_12 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 longistaminata	KN540387.1_FG001	1 retrocopy	retro_olon_12 ,