RetrogeneDB ID: retro_oruf_20

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 5:15821014..15821536(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI05G15670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G33000
• Aliases: None
• Description: None

Sequence

>retro_oruf_20
ATGGCCGGAGTAGGGAGGACGATGATCGCGCCGCTGCTGGTGCTGAATCTGATCATGTACTTGATCGTGATCGGGTTCGC
GAGCTGGAATCTCAACCACTACATCAACGGCGAGACCAACCACCCGGGGGTCGCCGGCAACGGCGCCACCTTCTACTTCC
TCGTCTTCGCCATCCTCGCGGGGGTGGTCGGCGCCGCCTCCAAGCTCGCCGGCGTCCACCACGTCCGCTCCTGGGGCGCG
CACAGCCTCGCCGCCGGCGCCGCGTCGGCGCTCATCGCCTGGGCCATCACCGCGCTCGCCTTCGGCCTCGCCTGCAAGGA
GATCCACATCGGCGGCTACCGCGGGTGGCGCCTCCGCGTGCTCGAGGCCTTCGTCATCATCCTCGCCTTCACGCAGCTGC
TCTACGTCGCCATGCTCCACGGCGGCCTCTTCTCCGGCAACCACGCCGCCGGCGCCGGCGGCTACGGCGGCGACTACCCC
GCCGACCACCACCACAAGCCCGCCGCCGCGGCCAGGGTCTAA

Alignment

ORF - retro_oruf_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.37 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRYIGPLLCVNLVMHAAVLGLAGWSLNKFIDGETHHH-LGGNTSSGYLLVFSLMAGVVGVCSVLPGLLHV
          R..I.PLL..NL.M...V.G.A.W.LN..I.GET.H....GN....Y.LVF...AGVVG..S.L.G..HV
Retrocopy RTMIAPLLVLNLIMYLIVIGFASWNLNHYINGETNHPGVAGNGATFYFLVFAILAGVVGAASKLAGVHHV

Parental  RAWRGETLAAAASTGLVSWALTALSFGLACKHITLGN-RGRRLRTLEAFIAILTLTQLLYLILLHTGSLG
          R.W....LAA.A...L..WA.TAL.FGLACK.I..G..RG.RLR.LEAF..IL..TQLLY...LH.G...
Retrocopy RSWGAHSLAAGAASALIAWAITALAFGLACKEIHIGGYRGWRLRVLEAFVIILAFTQLLYVAMLHGGLFS

Parental  SSMTLG
          .....G
Retrocopy GNHAAG

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_20 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_67451	1 retrocopy	retro_hvul_11,
Oryza rufipogon	ORUFI02G33000	1 retrocopy	retro_oruf_20 ,