RetrogeneDB ID: retro_olon_10

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538856.1:50864..51797(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538856.1_FG031
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN539849.1_FG007
• Aliases: None
• Description: None

Sequence

>retro_olon_10
ATGGAGGGATCCGCAGGGGCGCCGCTCCGCACGCGCGTGTGCATCATCGGGAGCGGGCCGTCGGCGCACACGGCGGCGAT
CTACGCCGCCCGCGCGGAGCTCAAGCCCGTGCTCTTCGAGGGCTGGCTCGCCAACGACATCGCGGCGGGGGGCCAGCTCA
CCACCACCACCGACGTCGAGAACTTCCCGGGGTTCCCCGAGGGGATCCTCGGCGGCGAGCTCATGGATCGGTGCCGCGCC
CAGTCCCTCCGGTTCGGCACCAGCATCATCTCCGAGACCGTCACCGCGGTCGACTTCTCCGCCCGCCCCTTCCGCGTCGC
CTCCGACTCCACCACCGTGCTCGCCGACGCCGTCGTCGTCGCCACCGGCGCCGTCGCCCGGCGACTCCACTTCGCCGGCT
CCGACGCCTACTGGAACCGCGGCATCTCCGCCTGCGCCGTCTGCGACGGGGCCGCCCCAATCTTCAGGAACAAACCCATC
GCCGTCATCGGCGGCGGCGACTCCGCCATGGAGGAGTCCAACTTCCTCACCAAGTACGGCTCCCATGTGTACATCATCCA
CCGCCGCAACACCTTCCGCGCCTCCAAGATCATGCAGGCCAGGGCGCTGTCAAACCCCAAGATCCAGGTCTTCTGGGACT
CTGAGGTCGTCGAGGCCTACGGCGGTGAGGGTGGAGGTCCATTGGCTGGTGTCAAGGTGAAGAACTTGGTTACTGGGAAG
ATCTCCGACCTTCAGGTGTCCGGGCTCTTCTTCGCCATCGGACATGAACCGGCGACCAAGTTTCTTGGTGGACAGCTTGA
GCTGGATGCTGATGGATATGTGGCCACCAAGCCAGGCTCCACGCACACCAGTGTGAAGGGGGTCTTTGCTGCTGGGGATG
TGCAGGACAAGAAGTATCGCCAGGCCATTACTGCCGCTGGATCAGGTTTGTGA

Alignment

ORF - retro_olon_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.53 %
• Parental protein coverage: 63.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIGSGPAGYTAAIYAARANLKPVVFEGYQVGGVP-GGQLMTTTEVENFPGFPDGVTGPDLMDKMRKQAER
          IIGSGP...TAAIYAARA.LKPV.FEG........GGQL.TTT.VENFPGFP.G..G..LMD..R.Q..R
Retrocopy IIGSGPSAHTAAIYAARAELKPVLFEGWLANDIAAGGQLTTTTDVENFPGFPEGILGGELMDRCRAQSLR

Parental  WGAELHQEDVEFVNVKSRPFVIRSSDREVKCHSVIIATGAAAKRLRLPREDEFWSRGISACAICDGASPL
          .G.....E.V..V....RPF...S....V....V..ATGA.A.RL.....D..W.RGISACA.CDGA.P.
Retrocopy FGTSIISETVTAVDFSARPFRVASDSTTVLADAVVVATGAVARRLHFAGSDAYWNRGISACAVCDGAAPI

Parental  FKGQVLAVVGGGDTATEEAIYLTKYARHVHLLVRKDQLRASKAMQDRVLNNPNITVHFNTEAVDVVSNP-
          F.....AV.GGGD.A.EE...LTKY..HV....R....RASK.MQ.R.L.NP.I.V....E.V.......
Retrocopy FRNKPIAVIGGGDSAMEESNFLTKYGSHVYIIHRRNTFRASKIMQARALSNPKIQVFWDSEVVEAYGGEG

Parental  KGQMSGIQLKRTDTGEESVLEVKGLFYGIGHTPNSQLLQGQIDLDDAGYILVEEGTAKTSVDGVFAAGDV
          .G...G...K...TG..S.L.V.GLF..IGH.P....L.GQ..LD..GY.....G...TSV.GVFAAGDV
Retrocopy GGPLAGVKVKNLVTGKISDLQVSGLFFAIGHEPATKFLGGQLELDADGYVATKPGSTHTSVKGVFAAGDV

Parental  QDHEWRQAVTAAGSG
          QD...RQA.TAAGSG
Retrocopy QDKKYRQAITAAGSG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza longistaminata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_10 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539849.1_FG007	1 retrocopy	retro_olon_10 ,