RetrogeneDB ID: retro_olon_2

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538756.1:83222..84587(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538756.1_FG054
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538756.1_FG066
• Aliases: None
• Description: None

Sequence

>retro_olon_2
ATGGCGGCGGCGGCGTGCGTGCTCGCCGTGGTGGTGGTGGTGCTGGCGTTCTTGTCCCCGGCGGCGCGCGGCGGCGTCAC
GAGCACGTACCGGAGGAGCCTGCAGGCGCTCCCAGACATGCCGATCGACGCCGACGTGTTCCGGCCGCCGCCCGGGTTCA
ACGCGCCGGAGCAGGTCCACATCACGCTGGGCGACCAGACCGGCCGCGCCATGACCGTCTCCTGGGTGACCCCGAAGCTC
CCCGACAGCAACGTCGTCCGCTACGGCCTCCGCGCCGACAACCTCACCCACACCGCCAATGGCACCTTCCGCCGCTACTC
CTTCGGGCGCAAGTACCGGTCGGGATTCATCCACCACGCCACCCTCACCGGCCTCGACTACGGCACCAAGTACCACTACG
CCGTCGGCTCCGGCGACACCGCCAGCGCCAGGTCCTTCTCCTTCACGACGCCGCCCAAGCCCGGGCCCGACGCGCCCTAC
AAGTTCGGGCTCATCGGCGACCTCGGGCAGACGTTCCACTCGAACGACACGCTGAGCCACTACGAGGCGTGCGGCGGCGA
CGCGGTGCTGTTCATCGGCGACCTGTCGTACGCGGACAACCACCCGGGGCACGACAACAACCGGTGGGACACGTGGGCGC
GGTTCGTGGAGCGGAGCGTGGCGTACCAGCCGTGGATCTGGACGACGGGGAACCACGAGCTGGACTTCGCGCCGGAGCTG
GGGGAGACGACGCCGTTCAAGCCGTTCACGAACAGGTACCCGACGCCGTTCGGGGCGTCGGGGAGCACGCGGCCGCTGTG
GTACTCGGTGAGGATGGCGTCGGCGCACGTGATCGTGCTGGCGTCGTACGCGGCGTACGGCAAGTACACGCCGCAGTGGA
GGTGGCTGGAGGGGGAGCTGAGGCGCGTGGACAGGGCGGTGACGCCATGGCTGATCGTGTGCGTGCACTCGCCGTGGTAC
AGCAGCAATGGCTACCACTACATGGAGGGGGAGTCGATGCGCGTGGAGTTCGAGCGGTGGCTCGTCGACGCCAAGGCCGA
CGTGGTGCTCGCCGGCCACGTCCACTCGTACGAGCGGACGCGGCGGGTGTCGAATGTGGCGTACGACATCGCCAACGGGA
TGGCCACGCCGGTGTACATCAACATCGGCGACGGGGGGAACATCGAGGGGCTCGCCGACGACTTCCGGTGGCCGCAGCCG
GACTACTCGGTGTTCCGGGAGGCCAGCTTCGGCCACGCCACGCTGCAGATCGTCAACCGGACGCACGCCTTCTACGAGTG
GCACCGCAACAGCGACGGCGTCAAGCTCGTCGCCGACCATGCCTGGTTCACCAACCGTTACTGGTTTCCCACTGACACCA
ACTAG

Alignment

ORF - retro_olon_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.86 %
• Parental protein coverage: 80.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHLLLLLLAAATWTCAGAGAGVTSEYRRKLEATVDMPLDADVFRVPPGYNAPQQVHITLGDQTGTAMTVS
          A..L.............A..GVTS.YRR.L.A..DMP.DADVFR.PPG.NAP.QVHITLGDQTG.AMTVS
Retrocopy ACVLAVVVVVLAFLSPAARGGVTSTYRRSLQALPDMPIDADVFRPPPGFNAPEQVHITLGDQTGRAMTVS

Parental  WVTANEMGSSTVRYGSSPEKLDRAAEGSHTRYDYFN-YTSGFIHHCTLTGLTHATKYYYAMGFAHTV--R
          WVT.....S..VRYG.....L...A.G...RY.....Y.SGFIHH.TLTGL...TKY.YA.G...T...R
Retrocopy WVTPKLPDSNVVRYGLRADNLTHTANGTFRRYSFGRKYRSGFIHHATLTGLDYGTKYHYAVGSGDTASAR

Parental  TFSFTTPPKPAPDAPFKFGLIGDLGQTFDSNSTLAHYEANGGDAVLFVGDLSYADNYPLHDNNRWDTWAR
          .FSFTTPPKP.PDAP.KFGLIGDLGQTF.SN.TL.HYEA.GGDAVLF.GDLSYADN.P.HDNNRWDTWAR
Retrocopy SFSFTTPPKPGPDAPYKFGLIGDLGQTFHSNDTLSHYEACGGDAVLFIGDLSYADNHPGHDNNRWDTWAR

Parental  FVERSVAYQPWIWTAGNHELDYEPELGETAPFKPFTHRYPTPYRAAGSTEPFWYSVKIASAHVIVLASYS
          FVERSVAYQPWIWT.GNHELD..PELGET.PFKPFT.RYPTP..A.GST.P.WYSV..ASAHVIVLASY.
Retrocopy FVERSVAYQPWIWTTGNHELDFAPELGETTPFKPFTNRYPTPFGASGSTRPLWYSVRMASAHVIVLASYA

Parental  AYGKYTPQWTWLQEELATRVDRKLTPWLIVLMHSPWYNSNNYHYMEGETMRVQFERWLVDAKVDVVLAGH
          AYGKYTPQW.WL..EL..RVDR..TPWLIV..HSPWY.SN.YHYMEGE.MRV.FERWLVDAK.DVVLAGH
Retrocopy AYGKYTPQWRWLEGEL-RRVDRAVTPWLIVCVHSPWYSSNGYHYMEGESMRVEFERWLVDAKADVVLAGH

Parental  VHSYERSRRFANIEYNIVNGKATP
          VHSYER.RR..N..Y.I.NG.ATP
Retrocopy VHSYERTRRVSNVAYDIANGMATP

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_2 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA035760	1 retrocopy	retro_oind_64,
Oryza longistaminata	KN538756.1_FG066	1 retrocopy	retro_olon_2 ,
Oryza sativa japonica	OS12G0637100	1 retrocopy	retro_osat_32,