RetrogeneDB ID: retro_opun_44

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 12:24244444..24244724(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G29700
• Aliases: None
• Description: None

Sequence

>retro_opun_44
GTAGCTCATTTGCCGCGTACTACGAAGAGATCGATCGATCTGCGCCATGTACAATGGGTGTTTCCGGAGAGTACTCCTAC
ACACGGTGTTAACTTTTTCAGCCGGAGCCATCTCCCAGCAGAAGATCATGATCTCTCTGTGAGGGACCGCCTCCCTACGC
TCCTCCATTCCTTTTCGTGGAGCCACGGAGCCGGGCTTCGTGTTGGACGCACCGTGGCTAGAGAAGTGGCTCGTGGACAC
CGTTCCAACCCCCCGGATTTTTCCCTTCCACCCCTCACCT

Alignment

ORF - retro_opun_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.46 %
• Parental protein coverage: 92.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LANTRTTTERE-SNHSMYNRCPWGVALLTVSPFSAGAVSQQRAVTPLRGTL-LPALLRSFSSSHGAGLRV
          .A....TT.R..S...MYN.C...V.L.TV..FSAGA.SQQ.....L.GT..LP.LL.SFS.SHGAGLRV
Retrocopy VAHLPRTTKRS>SICAMYNGCFRRVLLHTVLTFSAGAISQQKIMISL*GTA<LPTLLHSFSWSHGAGLRV

Parental  GRTVARGVARGHHSH-RWIFPFHPSP
          GRTVAR.VARGH.S....IFPFHPSP
Retrocopy GRTVAREVARGHRSN>PRIFPFHPSP

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_44 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 punctata	OPUNC01G29700	1 retrocopy	retro_opun_44 ,