RetrogeneDB ID: retro_opun_10

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 8:399677..400613(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC08G00420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC08G14380
• Aliases: None
• Description: None

Sequence

>retro_opun_10
ATGATGAACAGCTTCTACGCGTCCATCGGGCACGGCCTGGACGCGCTGCACCGCAGCCTGGCCGGCGGCGAGGTGGGGTT
CATGTCGGCGGCGTTCGTGCAGCAGGCGGCGGCGCTGCTCCGGTCGCTGCACTGGCAGGTGGTGCGCGTGGTGGAGCGGC
TGCACCTGCCGCCGGGGGAGAGGTGGCTGGACGAGTACATGGACGAGACCTCCCGCCTGTGGGACGCCTGCCACCTCGTC
CGCGCCGGCGCCTCCGCCCTCGACGCCTACTGCGCCGCCGCCGCCCACGCCCTCCACGACCTCCACCACAACCCACGCCA
CGCCGCCCGCGCCATCAACGCCCCTCGCCGCCACGCCGCCGGCCTCCTCCAGGAGAACCGCGCCCTCCTCGCCGACGCCC
GCCTCGACCCGGCCTCCCTCCTCCTCGACCACCGCTCCCCGCGAGACTTCAACCTCAACGCCTTCAATGGCTTCCGCGCA
GTCCTCTACGCGCTCCGCAACGCCACCTCCTTCCTCCTCGCCCTCCTCCTCTCCGCCACCGTCTCCTCCCTCCCCGACCA
CCTCTCCTCCTGCGGAGGGCCCACCGCATCCGCAGGCGGAGGCGGAGGCGGCTACGTCTCCTCCATGGCGCGCCTCCGCC
AGCGCGTCGCCGACGAGATGGACGCCATCGCCCACTGCGGCCACGACGGCATCTTGATGTACGAGTTCCGGCAGGCCAGG
GCGGGCATCGAGGGCCTCAAGGCGGAGCTGGACAGGGTGGTGGCCACCGGCGGGTACGATGACCCGGAGGAGATGGCGGA
GAGGGCGGAGGTCGTCAAAGGGTGGGTGGCCATGCTCAGGTCGGGCGCCGAGGCCGTCATCGCCGAGCTCGACGACTTCT
TCGATGACATTGTCCAAGGCAGGAAGCTGCTCTCCGACCTCTGCAGCCATCGCTGA

Alignment

ORF - retro_opun_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.23 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CDGVFVGSGVFKSVGIAAACDCTTPRRTWQQATHSPNHPHRLELGGIEMENRSIVDAHLDPASLLLDLRS
          C..V..G.........AAA............A....N.P.R...G..........DA.LDPASLLLD.RS
Retrocopy CHLVRAGASALDAYCAAAAHALHDLHHNPRHAARAINAPRRHAAGLLQENRALLADARLDPASLLLDHRS

Parental  SLDFNLNDFCG---VLYALRNATSFLLALLISVIVSCLLDHLCCALVPLPTIAAG---YVSSMARLCQHV
          ..DFNLN.F.G...VLYALRNATSFLLALL.S..VS.L.DHL.....P......G...YVSSMARL.Q.V
Retrocopy PRDFNLNAFNGFRAVLYALRNATSFLLALLLSATVSSLPDHLSSCGGPTASAGGGGGGYVSSMARLRQRV

Parental  TEEMDAIANDHFSNDDIMMYEFWQTRADIESLKVELDRVVAT-GYDDLEEMAERAKLVKGW
          ..EMDAIA..H...D.I.MYEF.Q.RA.IE.LK.ELDRVVAT.GYDD.EEMAERA..VKGW
Retrocopy ADEMDAIA--HCGHDGILMYEFRQARAGIEGLKAELDRVVATGGYDDPEEMAERAEVVKGW

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_10 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	OPUNC08G14380	1 retrocopy	retro_opun_10 ,