RetrogeneDB ID: retro_oruf_13

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 12:23513268..23514441(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI12G22620
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI03G33430
• Aliases: None
• Description: None

Sequence

>retro_oruf_13
ATGGCGGACGCTGATGACATCCAGCCTCTGGTGTGCGACAACGGGACGGGGATGGTGAAGGCCGGGTTCGCGGGGGACGA
CGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGGAGGCCACGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG
CGTACGTCGGGGACGAGGCGCAGTCGAAGAGAGGCATCCTGACGCTCAAGTACCCCATCGAGCACGGCATCGTCAACAAC
TGGGACGACATGGAGAAGATATGGCACCACACCTTCTACAACGAGCTCCGCGTTGCCCCCGAGGAGCACCCGGTGCTGCT
GACGGAGGCCCCCCTCAACCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTCGAGACCTTCAACGCCCCCGCCA
TGTACGTCGCCATCCAGGCCGTCCTCTCCCTCTACGCCAGCGGCCGCACCACCGGCATCGTCCTCGACTCCGGCGACGGC
GTCAGCCACACCGTCCCCATCTACGAGGGCTACGCCCTCCCCCACGCCATCCTCCGCCTCGACCTCGCCGGCCGCGACCT
CACCGACTACCTCATGAAGATCCTCACCGAGCGCGGCTACTCCTTCACCACCACCGCCGAGCGCGAGATCGTCCGCGACG
TCAAGGAGAAGCTCTCCTACATCGCCCTCGACTTCGACCAGGAGATGGCCACCGCCGCCACGGGGTCGTCCGTCGAGAAG
AGCTACGAGCTGCCCGACGGCCAGGTCATCACCATCGGCGCCGAGAGGTTCCGCTGCCCCGAGGTGCTGTTCCAGCCCTC
CTTCGTGGGGATGGAGGCTGCGGGGATCCACGAGACCACCTACAACTCCATCATGAAGTGCGACGTCGACATCCGCAAGG
ATCTCTACGGCAACATCGTCCTCAGCGGTGGCACCACCATGTTCCCCGGCATCGCCGACAGGATGAGCAAGGAGATCACC
GCCCTCGCTCCCAGCAGCATGAAGATCAAGGTCGTCGCGCCGCCCGAGAGGAAGTACTCCGTCTGGATCGGAGGCTCCAT
CCTCGCATCACTCAGCACCTTCCAGCAGGCACGCACCCGGCCGCCCACTCCTTTCTTTCCTTACTTCTTACTATTATTTT
CCACATTAATACTATATACTCCGCTTCATGCAGATGTGGATTGCCAAGGCTGA

Alignment

ORF - retro_oruf_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.47 %
• Parental protein coverage: 94.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADAEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEAQSKRGILTLK
          MADA.DIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEAQSKRGILTLK
Retrocopy MADADDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEAQSKRGILTLK

Parental  YPIEHGIVSNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQA
          YPIEHGIV.NWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFN.PAMYVAIQA
Retrocopy YPIEHGIVNNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNAPAMYVAIQA

Parental  VLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI
          VLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI
Retrocopy VLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI

Parental  VRDMKEKLSYIALDYDQEMETAKTSSSVEKSYELPDGQVITIGAERFRCPEVLFQPSFIGMEAAGIHETT
          VRD.KEKLSYIALD.DQEM.TA.T.SSVEKSYELPDGQVITIGAERFRCPEVLFQPSF.GMEAAGIHETT
Retrocopy VRDVKEKLSYIALDFDQEMATAATGSSVEKSYELPDGQVITIGAERFRCPEVLFQPSFVGMEAAGIHETT

Parental  YNSIMKCDVDIRKDLYGNIVLSGGTTMFPGIADRMSKEITALAPSSMKIKVVAPPERKYSVWIGGSILAS
          YNSIMKCDVDIRKDLYGNIVLSGGTTMFPGIADRMSKEITALAPSSMKIKVVAPPERKYSVWIGGSILAS
Retrocopy YNSIMKCDVDIRKDLYGNIVLSGGTTMFPGIADRMSKEITALAPSSMKIKVVAPPERKYSVWIGGSILAS

Parental  LSTFQQ
          LSTFQQ
Retrocopy LSTFQQ

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_13 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA013463	1 retrocopy	retro_oind_29,
Oryza rufipogon	ORUFI03G33430	1 retrocopy	retro_oruf_13 ,