RetrogeneDB ID: retro_oruf_38

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 1:8898721..8899426(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI01G12030
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI05G21470
• Aliases: None
• Description: None

Sequence

>retro_oruf_38
ATGGCCGCGGAGGTCGCCGCCGGCGGCGACTCCGGCTGGAGCAGCGGCAGCGCGACGTTCTACGGCGGCAGCGACGCGTC
GGGGACGATGGGTGGCGCGTGCGGGTACGGCAACCTGTACAGCGCCGGGTACGGGACGAGCACGGCGGCGCTGAGCACGG
CGCTGTTCAACAACGGGCAGAGCTGCGGCGCGTGCTTCGAGGTCCGGTGCGGCGGCGGCGGCAGCTGCCTCGCCGGCACC
GTGGCGGTGACGGCCACCAACCTCTGCCCGCCCAACTACGCGCTCGCCGGCGACGCCGGCGGGTGGTGCAACCCGCCGCG
GCCGCACTTCGACATGGCGGAGCCGGCGTTCACCAGGATCGCGCAGGCCCGCGCCGGCGTGGTGCCGGTGCAGTACCGGC
GCGTGGCGTGCGCGAAGCAGGGCGGCATCCGGTTCACCATCACCGGCCACTCCTACTTCAACCTGGTGCTCGTCACCAAC
GTCGGCGGCGCCGGCGACGTGACGGCGGTGTCGGTGAAGGGGTCGCGGTCGGGGTGGCAGGCCATGAGCCACAACTGGGG
CGCCAACTGGCAGAACGGCGCCAACCTCGACGGCCAGCCGCTCTCCTTCAGGGTCACCGCCAGCGACGGCCGCACCGTCA
CCTCCGACAACGTCGCCCCCTCCGGCTGGTCCTTCGGCCAGACCTTCTCCGGCGGCCAGTTCTAG

Alignment

ORF - retro_oruf_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.62 %
• Parental protein coverage: 95.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LARQASAAGYGGWQSAHATFYGGGDASGTMGGACGYGNLYSQGYGTNTAALSTALFNDGAACGSCYELRC
          .A....A.G..GW.S..ATFYGG.DASGTMGGACGYGNLYS.GYGT.TAALSTALFN.G..CG.C.E.RC
Retrocopy MAAEVAAGGDSGWSSGSATFYGGSDASGTMGGACGYGNLYSAGYGTSTAALSTALFNNGQSCGACFEVRC

Parental  DNAGSSCLPGSITVTATNFCPPNYGLPSDDGGWCNPPRPHFDMAEPAFLHIAQYRAGIVPVSFRRVPCVK
          ...G.SCL.G...VTATN.CPPNY.L..D.GGWCNPPRPHFDMAEPAF..IAQ.RAG.VPV..RRV.C.K
Retrocopy -GGGGSCLAGTVAVTATNLCPPNYALAGDAGGWCNPPRPHFDMAEPAFTRIAQARAGVVPVQYRRVACAK

Parental  KGGIRFTVNGHSYFNLVLVTNVAGAGDVRSVSIKGSRTGWQPMSRNWGQNWQSNAFLDGQSLSFQVTASD
          .GGIRFT..GHSYFNLVLVTNV.GAGDV..VS.KGSR.GWQ.MS.NWG.NWQ..A.LDGQ.LSF.VTASD
Retrocopy QGGIRFTITGHSYFNLVLVTNVGGAGDVTAVSVKGSRSGWQAMSHNWGANWQNGANLDGQPLSFRVTASD

Parental  GRTVTSNNVAHPGWQFGQTFEGGQF
          GRTVTS.NVA..GW.FGQTF.GGQF
Retrocopy GRTVTSDNVAPSGWSFGQTFSGGQF

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_38 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017864	1 retrocopy	retro_oind_17,
Oryza barthii	OBART05G20250	1 retrocopy	retro_obar_16,
Oryza glumaepatula	OGLUM05G21340	1 retrocopy	retro_oglu_10,
Oryza rufipogon	ORUFI05G21470	1 retrocopy	retro_oruf_38 ,
Oryza sativa japonica	OS05G0477600	1 retrocopy	retro_osat_6,