RetrogeneDB ID: retro_oruf_14

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:8655822..8656626(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G12580
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI10G18850
• Aliases: None
• Description: None

Sequence

>retro_oruf_14
ATGGCATCCTCTTGTCTCCTTCTGGCCTGTGTCGTGGCAGCGGCCATGGTGTCTGCAGTGTCATGTGGGCCGCCCAAGGT
GCCGCCTGGCCCCAACATCACTGCGGCCTACGGCAAACAGTGGTTGGAAGCTAGGGGTACCTGGTACGGCAAGCCAAAGG
GTGCCGGCCCCAACGACAACGGCGGCGCTTGCGGGTACAAGGACGTTGACAAGGCTCCCTTCCTCGGCATGAACTCATGT
GGCAATGACCCTATCTTCAAGGATGGCAAGGGCTGCGGCTCCTGCTTTGAGGTCAAGTGTTCCAAGCCAGAGGCCTGCTC
CGACAAGCCCGTCATCATCCACATCACCGACATGAACACCGAGCCTATCGCCGCCTACCACTTCGACCTCTCTGGCCATG
CTTTCGGTGCCATGGCTAAGGAAGGCAAGGATGAGGAACTCCGCAAGGCGGGAATTATCGATATGCAGTTTCGTCGCGTC
CGCTGCAAGTACCCTGGTGAGACTAAGGTCACCTTCCACGTTGAGAAGGGCTCCAACCCCAACTACTTTGCGGTGCTTGT
CAAGTACGTCGGTGGTGACGGTGACGTCGTGAAGGTGGAACTTAAGGAGAAAGGCTCTGAGGAGTGGAAGCCACTCAACG
AGTCATGGGGTGCTATTTGGAGGATAGACACTCCCAAGCCACTCAAGGGCCCCTTCTCCCTCCGTGTCACCACCGAGTCT
GACCAGAAGCTTGTCGCCAACGACGTCATCCCCAATAATTGGAAGGCCGACGCTCTCTACAAATCAGAGATCCAAGTCGA
CTAA

Alignment

ORF - retro_oruf_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.08 %
• Parental protein coverage: 96.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IVLAVAVVAALVGGGSCGPPKVPPGPNITTNYNAPWLPARATWYGQPYGSGPTDNGGACGIKNVNLPPYN
          ..LA..V.AA.V...SCGPPKVPPGPNIT..Y...WL.AR.TWYG.P.G.GP.DNGGACG.K.V...P..
Retrocopy LLLACVVAAAMVSAVSCGPPKVPPGPNITAAYGKQWLEARGTWYGKPKGAGPNDNGGACGYKDVDKAPFL

Parental  GMISCGNVPIFKDGRGCGSCYEVKCEQPAACSKQPVTVFITDMNYEPISAYHFDFSGKAFGAMACPGKET
          GM.SCGN.PIFKDG.GCGSC.EVKC..P.ACS..PV...ITDMN.EPI.AYHFD.SG.AFGAMA..GK..
Retrocopy GMNSCGNDPIFKDGKGCGSCFEVKCSKPEACSDKPVIIHITDMNTEPIAAYHFDLSGHAFGAMAKEGKDE

Parental  ELRKAGIIDMQFRRVRCKYPGGQKVTFHVEKGSNPNYLAVLVKFVADDGDVIQMDLQEAGLPAWRPMKLS
          ELRKAGIIDMQFRRVRCKYPG..KVTFHVEKGSNPNY.AVLVK.V..DGDV....L.E.G...W.P...S
Retrocopy ELRKAGIIDMQFRRVRCKYPGETKVTFHVEKGSNPNYFAVLVKYVGGDGDVVKVELKEKGSEEWKPLNES

Parental  WGAIWRMDTATPLKAPFSIRVTTESGKSLIAKDVIPVNWMPDAIYVSNVQ
          WGAIWR.DT..PLK.PFS.RVTTES...L.A.DVIP.NW..DA.Y.S..Q
Retrocopy WGAIWRIDTPKPLKGPFSLRVTTESDQKLVANDVIPNNWKADALYKSEIQ

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_14 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza rufipogon	ORUFI10G18850	1 retrocopy	retro_oruf_14 ,
Oryza rufipogon	ORUFI10G19380	1 retrocopy	retro_oruf_30,
Physcomitrella patens	PP1S100_99V6	1 retrocopy	retro_ppat_8,