RetrogeneDB ID: retro_oruf_16

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:34397617..34398460(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G43640
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI04G05780
• Aliases: None
• Description: None

Sequence

>retro_oruf_16
ATGGCTGCAGGCAGCGGCAGCGGCAGCAATCCTAAGGACTACCAGGATCCTCCTCCCGCGCCGCTGGTGGACACCGGCGA
GCTAGGTAAGTGGTCACTGTATCGCGCCGCCATTGCGGAGTTCACAGCCACGCTGCTGTTGGTGTGCATCAGTGTGAGCA
CCGTGATCGGTGAGAAGCGGCAGTCGGGCGAGGGCGGCGCCGGCGTGCTTGGCATTGCCTGGGCCTTTGGTGGCCTCATC
TTCGTGCTGGTGTACTGCACCGCTGGCATCTCCGGGGGGCACATGAACCCAGCCGTGACCTTCGCCATGGTGCTCGCGCG
AAGGGTGTCGCTGCCGCGAGCGGCGCTGTACACGATGGCGCAGTGCGTGGGCGCCGTGTGCGGCGCAGGGCTCGCCAGGG
CGATGCACGGTGGCGGGCAGTACGCGCGGCACGGCGGAGGTGCCAACGAGCTGGCGGCGGGCTACTCGGCGGGGGCAGGG
GTCGTGGCGGAGATGGTGGGCACGTTCGTGCTGGTGTACACGGTGTTCTCGGCGACGGACCCGAAGCGGAAGGCCAGGGA
CTCTCACGTGCCGGTGCTGGCGCCGCTTCCCATCGGGTTGGCGGTGCTGGTTGTGCACCTTGCCACCATCCCCATCACCG
GCACTGGCATCAACCCCGCCCGCAGCCTTGGCCCCGCCCTCGTCCTCGGCCTCGGCACCACCAAGGCCTGGTCTCACCTC
TGGATCTTCTGGGTGGGCCCCTTCGCCGGCGCCGCCGCCGCAATGATCTACCATCACTACATCCTCAGGGGCGCTGCCGC
CAAGGCCTTCGCCTCCTCCTCCTACCGATCACCCCATTTTTAA

Alignment

ORF - retro_oruf_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 92.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKDYTDPPPAPLFDVGELRLWSFYRALIAEFIATLLFLYITVATVIGYKVQSSADQCGGVGTLGIAWAFG
          PKDY.DPPPAPL.D.GEL..WS.YRA.IAEF.ATLL...I.V.TVIG.K.QS.....GG.G.LGIAWAFG
Retrocopy PKDYQDPPPAPLVDTGELGKWSLYRAAIAEFTATLLLVCISVSTVIGEKRQSGE---GGAGVLGIAWAFG

Parental  GMIFILVYCTAGISGGHINPAVTFGLLLARKVSVIRAVMYIVAQCLGGIVGVGIVKGIMKH-QYNANGGG
          G.IF.LVYCTAGISGGH.NPAVTF...LAR.VS..RA..Y..AQC.G...G.G.........QY...GGG
Retrocopy GLIFVLVYCTAGISGGHMNPAVTFAMVLARRVSLPRAALYTMAQCVGAVCGAGLARAMHGGGQYARHGGG

Parental  ANMVASGYSTGTALGAEIIGTFVLVYTVFSATDPKRNARDSHVPVLAPLPIGFAVFMVHLATIPITGTGI
          AN..A.GYS.G....AE..GTFVLVYTVFSATDPKR.ARDSHVPVLAPLPIG.AV..VHLATIPITGTGI
Retrocopy ANELAAGYSAGAGVVAEMVGTFVLVYTVFSATDPKRKARDSHVPVLAPLPIGLAVLVVHLATIPITGTGI

Parental  NPARSIGAAVI--YNQKKAWDDHWIFWAGPFIGALAAAAYHQYILRAAAIKALGS
          NPARS.G.A........KAW...WIFW.GPF.GA.AA..YH.YILR.AA.KA..S
Retrocopy NPARSLGPALVLGLGTTKAWSHLWIFWVGPFAGAAAAMIYHHYILRGAAAKAFAS

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_16 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009362	1 retrocopy	retro_oind_43,
Oryza longistaminata	KN540828.1_FG001	1 retrocopy	retro_olon_7,
Leersia perrieri	LPERR04G03430	1 retrocopy	retro_lper_22,
Oryza brachyantha	OB0038G10090	1 retrocopy	retro_obra_3,
Oryza barthii	OBART04G05050	1 retrocopy	retro_obar_18,
Oryza glumaepatula	OGLUM04G04240	1 retrocopy	retro_oglu_29,
Oryza meridionalis	OMERI04G05010	1 retrocopy	retro_omer_6,
Oryza nivara	ONIVA04G03300	1 retrocopy	retro_oniv_20,
Oryza punctata	OPUNC04G04310	1 retrocopy	retro_opun_34,
Oryza rufipogon	ORUFI04G05780	1 retrocopy	retro_oruf_16 ,
Oryza sativa japonica	OS04G0233400	1 retrocopy	retro_osat_19,