RetrogeneDB ID: retro_oruf_23

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 6:2619077..2619404(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI06G03780
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G02720
• Aliases: None
• Description: None

Sequence

>retro_oruf_23
ATGGGGAAGAGGAAGTCTCGGGTGTCGAAGATGCTGGCGACGGCGAAGAAGGCGGCGCCGAAGCTGGAGACGGCGTTCAG
CTGCCCGTTCTGCGACCACGGCGGCGCGGTGGAGTGCAGCATCGACATCAAGCACATGATCGCCGAGGCCTCCTGCTTCG
TCTGCCAGGCGCGCTACTCCACCACCGCCCACGCGCTCACCGAGCCCATCGACGTCTACAGCGAGTGGATCGACCAGTGC
GAGCTCTCCAAAGCCGCCGCCGCCGCCGGCGACGACGACGACGACCACCACCACCACCACCACCGCAAGACCAAGCGCCG
CAGCTAA

Alignment

ORF - retro_oruf_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 74.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRK---SKAKPPPKKRMDKLDTVFCCPFCNHGSSVECRIDLKNLIGEASCRICLETFSTSVNALTEPI
          MGKRK...SK.....KK...KL.T.F.CPFC.HG..VEC.ID.K..I.EASC..C....ST...ALTEPI
Retrocopy MGKRKSRVSKMLATAKKAAPKLETAFSCPFCDHGGAVECSIDIKHMIAEASCFVCQARYSTTAHALTEPI

Parental  DIYSEWIDECE
          D.YSEWID.CE
Retrocopy DVYSEWIDQCE

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_23 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Musa acuminata	GSMUA_Achr4G31010_001	1 retrocopy	retro_macu_1,
Oryza punctata	OPUNC02G02130	1 retrocopy	retro_opun_14,
Oryza rufipogon	ORUFI02G02720	1 retrocopy	retro_oruf_23 ,
Solanum tuberosum	PGSC0003DMG400031773	2 retrocopies	retro_stub_147, retro_stub_148,
Prunus persica	PRUPE_ppa014081mg	1 retrocopy	retro_pper_27,