RetrogeneDB ID: retro_oruf_5

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 7:32060..33752(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI07G00060
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI03G33580
• Aliases: None
• Description: None

Sequence

>retro_oruf_5
ATGGAGGCGACGACGACTGACGGCACGACGGACCACGCGGGGAAACCGGCGGTGAGGAGCAAGAGCGGGACGTGGAGGGC
GTGCCCGTTCATCCTGGGGAACGAGTGCTGCGAGCGCCTGGCCTACTACGGCATGAGCGCCAACCTCGTCAACTACATGG
TCGATCGCCTCCGCCAGGGCAACGCCGGCGCCGCCGCCAGCGTCAACAACTGGTCCGGCACATGCTACGTCATGCCCCTC
GTCGGCGCCTTCCTCGCCGACGCCTACCTCGGTCGCTACCGCACCATCGCCGCGTTCATGGCGCTCTACATCGTCGGCCT
CGCGCTCCTCACCATGAGCGCCTCCGTGCCAGGCATGAAGCCGCCTAACTGCGCCACAATATCCGCCTCCTCGTGCGGGC
CCTCCCCAGGCCAGAGCGCCGCCTTCTTCGTCGCGCTCTACCTCATCGCCCTGGGCACCGGCGGGATCAAGCCCTGCGTC
TCCTCCTTCGGCGCCGACCAGTTCGACGACGCCGACCCACGCGAGCACCGGAGCAAGGCCTCCTTCTTCAACTGGTTCTA
CATGTCCATCAACGTCGGCGCCCTGGTGGCGTCGTCGGTGCTCGTCTGGGTGCAGATGAACGTGGGCTGGGGGTGGGGCT
TCGGCATCCCGGCCGTGGCCATGGCCGTGGCCGTCGCCAGCTTCCTCATGGGGAGCAGCCTCTACAGGCACCAGAAGCCC
GGGGGGAGCCCGCTCACCAGGATGCTGCAGGTGGTCGTGGCCGCCGCCAGGAAGTCAAGGGTGGCGCTGCCCGCCGACGC
CGCCGCGCTACTCTACGAGGGCGACAAGCTGGCCTGCGGGACGCGGCGGCTGGCTCACACGGAGCAGTTCAGGTGGCTGG
ACCGGGCTGCGGTGGTGACACCGACGACGGACAAGGACGACGACACCGGCAGCAGGTGGCGGCTGTGCCCGGTGACGCAG
GTGGAGGAGCTCAAGGCGGTGGTGCGGCTGCTGCCGGTGTGGGCGAGCGGGATCGTGATGTCGGCGGTGTACGGGCAGAT
GAGCACCATGTTCGTGCTGCAGGGGAACACGCTGGACCCTCGCATGGGCGCCACCTTCAAGATCCCCTCGGCGTCGCTCT
CCATCTTCGACACCCTCGCCGTCCTCGCCTGGGTCCCCGTCTACGACCGCCTCATCGTCCCCGCCGCCCGCCGCTTCACC
GGCCACCCGCGCGGCTTCACGCAGCTCCAGCGCATGGGCATCGGCCTCCTCATCTCCGTCTTCTCCATGGTGGCCGCCGG
GGTGCTGGAGGTGGTGCGCCTCCGCGTCGCCGCCGCCCACGGCATGCTCGACTCCACCTCCTACCTGCCCATCTCCATCT
TCTGGCAGGTGCAGTACTTCATCATCGGCCAGATCGACTTCTTCTACGACCAGGCGCCCGACGACATGCGCAGCACGTGC
ACCGCGCTCTCGCTCACCTCCTCCGCGCTCGGCAACTACCTCAGCACGCTGCTCGTCGTCATCGTCACCGCCGCATCCAC
CAGGGGCGGCGGCCTCGGATGGATCCCCGACAACCTCAACCGCGGCCACCTCGACTACTTCTTCTGGCTGCTCGCCGCGC
TCAGTGCTGTCAACTTCCTCGTCTACCTCTGGATCGCCAACTGGTACAGGTGCAAGACAATCACCACCACTGAAGCAGCC
GCTCAGACTTGA

Alignment

ORF - retro_oruf_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.4 %
• Parental protein coverage: 78.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGDGSVDFSGNPVVKERTGRWRACPFILGNECCERLAYYGISTNLVTYLTKKLHDGNASAASNVTAWQGT
          T.DG..D..G.P.V....G.WRACPFILGNECCERLAYYG.S.NLV.Y....L..GNA.AA..V..W.GT
Retrocopy TTDGTTDHAGKPAVRSKSGTWRACPFILGNECCERLAYYGMSANLVNYMVDRLRQGNAGAAASVNNWSGT

Parental  CYLTPLIGAILADAYWGRYWTIATFSMIYFIGMAVLTLSASVPTFMPPPC---EGSFCPPANPLQYTVFF
          CY..PL.GA.LADAY.GRY.TIA.F...Y..G.A.LT.SASVP...PP.C.....S.C.P..P.Q...FF
Retrocopy CYVMPLVGAFLADAYLGRYRTIAAFMALYIVGLALLTMSASVPGMKPPNCATISASSCGPS-PGQSAAFF

Parental  LGLYLIALGTGGIKPCVSSFGADQFDDTDPVERIQKGSFFNWFYFSINIGALISSSFLVWVQDNIGWGIG
          ..LYLIALGTGGIKPCVSSFGADQFDD.DP.E...K.SFFNWFY.SIN.GAL..SS.LVWVQ.N.GWG.G
Retrocopy VALYLIALGTGGIKPCVSSFGADQFDDADPREHRSKASFFNWFYMSINVGALVASSVLVWVQMNVGWGWG

Parental  FGIPTIFMGLAIISFFSGTSLYRFQKPGGSPITRVCQVVVASFRKWNVHVPEDSSRLYELPDGASAIEGS
          FGIP...M..A..SF..G.SLYR.QKPGGSP.TR..QVVVA..RK..V..P.D...L..L..G.....G.
Retrocopy FGIPAVAMAVAVASFLMGSSLYRHQKPGGSPLTRMLQVVVAAARKSRVALPADAAAL--LYEGDKLACGT

Parental  RQLEHTDELRCLDKAATITDLDVKADSFTNPWQICTVTQVEELKILVRMFPVWATTIVFSAVYAQMSTMF
          R.L.HT...R.LD.AA..T....K.D.....W..C.VTQVEELK..VR..PVWA..IV.SAVY.QMSTMF
Retrocopy RRLAHTEQFRWLDRAAVVTPTTDKDDDTGSRWRLCPVTQVEELKAVVRLLPVWASGIVMSAVYGQMSTMF

Parental  VEQGMMLDTSVG-PFKIPPASLSTFDVVSVIIWVPLYDSILVPIARRFTGNPRGFTELQRMGIGLVISIF
          V.QG..LD...G..FKIP.ASLS.FD...V..WVP.YD...VP.ARRFTG.PRGFT.LQRMGIGL.IS.F
Retrocopy VLQGNTLDPRMGATFKIPSASLSIFDTLAVLAWVPVYDRLIVPAARRFTGHPRGFTQLQRMGIGLLISVF

Parental  SMAAAAVLEIKRLDIARAEHLVDQNVPVPLNICWQIPQYFLVGASEVF
          SM.AA.VLE..RL..A.A....D.....P..I.WQ..QYF..G....F
Retrocopy SMVAAGVLEVVRLRVAAAHGMLDSTSYLPISIFWQV-QYFIIGQIDFF

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_5 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009904	1 retrocopy	retro_oind_36,
Hordeum vulgare	MLOC_58062	1 retrocopy	retro_hvul_66,
Oryza glumaepatula	OGLUM02G34910	1 retrocopy	retro_oglu_17,
Oryza glaberrima	ORGLA03G0409900	1 retrocopy	retro_ogla_29,
Oryza rufipogon	ORUFI03G33580	1 retrocopy	retro_oruf_5 ,
Oryza sativa japonica	OS03G0719900	1 retrocopy	retro_osat_25,
Triticum aestivum	Traes_4AL_59D5504B1	1 retrocopy	retro_taes_96,