RetrogeneDB ID: retro_olon_17

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538986.1:56956..57874(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538986.1_FG025
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN539266.1_FG011
• Aliases: None
• Description: None

Sequence

>retro_olon_17
ATGTGGTGGTCCAAGTTCCACTCGAACAAGCTCAAGTACACGCGTGGGTACCTGATCGAGGTGATGCACTCGGACACGGT
GGTGATATCGAACGTGACGCTGGTGAACTCGCCGGCGTGGAACATCCACCCTGTGTACAGCAGCAACATCGTGGTGCAGG
GGGTGACGATCCTGGCGCCGACGCACTCGCCCAACACCGACGGCATCAACCCGGACTCGTGCTCCCACGTCCGCATCGAG
GACTGCTACATCGTGTCCGGCGACGACTGCGTGGCGATCAAGTCCGGGTGGGACGAGTACGGGATCGCGTACGGGATGCC
CAGCCAGCACATCGTGGTGCGGAGGCTGACGTGCGTGTCGCCGACGAGCGCGGTGATCGCGCTGGGCAGCGAGATGTCGG
GCGGGATCAGCGACGTGCGGGCGGAGGACATAACGGCGGTGAACTCGGAGTCGGCGGTGCGGATCAAGACGGCGGTGGGG
CGCGGGGCGTACGTGCGCGACGTGTTCGTCCGGGGGATGTCGCTGGACACCATGAAGTGGGTGTTCTGGATGACGGGGAA
CTACAAGTCCCACCCGGACGACGGCTACGATCCCAACGCCATCCCCGTCGTCGACAACATCAGCTACCAGGACGTGGTGG
CCACGGGCGTCTACAAGGAGGCCGCCAGGCTGGAGGGCATCCAGGGCGCGCCCTTCCGCGGCATCTGCATCGCCAACGTC
ACCGCCACGCTCTCCAAGTCCCGCAAGTACCCCTGGACTTGCACCGACATCGAGGGGGTGTCCACCGGCGTCACGCCGGC
GCCGTGCGAGCCGCTGCAGGGGGCGCACGACGGCGCCTGCCCGTTCCCGACGGACACGCTGCCCATCGACCAGCTCGTCA
TGCAGCAGTGCGCCTACTCCGTCCCGGCCTCCATCTAG

Alignment

ORF - retro_olon_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61. %
• Parental protein coverage: 72.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VWWDKFHAKELTYTRGYLLELLYSNNIIISNVTFVDSPSWNLHPTYCTNVTISGITILAPLNSPNTDGID
          .WW.KFH...L.YTRGYL.E...S....ISNVT.V.SP.WN.HP.Y..N....G.TILAP..SPNTDGI.
Retrocopy MWWSKFHSNKLKYTRGYLIEVMHSDTVVISNVTLVNSPAWNIHPVYSSNIVVQGVTILAPTHSPNTDGIN

Parental  PDSSSHVKIEDSYIVSGDDCIAVKSGWDQYGIKFNMPSQHILIRRLTCISPTSAMIALGSEMSGGIRDVR
          PDS.SHV.IED.YIVSGDDC.A.KSGWD.YGI...MPSQHI..RRLTC.SPTSA.IALGSEMSGGI.DVR
Retrocopy PDSCSHVRIEDCYIVSGDDCVAIKSGWDEYGIAYGMPSQHIVVRRLTCVSPTSAVIALGSEMSGGISDVR

Parental  AVDNVAIDTESAVRIKSGVGRGGYVKDVFVRGLSLHTMKWVFWMTGNYGQHPDNSSDPNALPEVTGINYS
          A.D..A...ESAVRIK..VGRG.YV.DVFVRG.SL.TMKWVFWMTGNY..HPD...DPNA.P.V..I.Y.
Retrocopy AEDITAVNSESAVRIKTAVGRGAYVRDVFVRGMSLDTMKWVFWMTGNYKSHPDDGYDPNAIPVVDNISYQ

Parental  DVFAENV-TMAGRMEGIPNDPYTGICMSNVTAQLAPDAKKLQWNCTDVKGVASDVSPVPC-PELGAAGKP
          DV.A..V...A.R.EGI...P..GIC..NVTA.L.....K..W.CTD..GV...V.P.PC.P..GA....
Retrocopy DVVATGVYKEAARLEGIQGAPFRGICIANVTATLS-KSRKYPWTCTDIEGVSTGVTPAPCEPLQGAHDGA

Parental  CAFPEEELVIGPPELPTCSY
          C.FP...L.I.......C.Y
Retrocopy CPFPTDTLPIDQLVMQQCAY

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_17 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539266.1_FG011	1 retrocopy	retro_olon_17 ,
Oryza punctata	OPUNC03G01760	1 retrocopy	retro_opun_2,