RetrogeneDB ID: retro_olon_13

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN540067.1:2238..4221(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN540067.1_FG006
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538684.1_FG046
• Aliases: None
• Description: None

Sequence

>retro_olon_13
ATGCAGCTCGGGCTGTTCCTCGCCGCGCTTCTCCTCTTCACGTCTGTGGCGGCGGCCAAGGGTGGTGGTGCCAAGAGCGG
CGGCGGCACCGTGATCGGGATCGACCTCGGCACGACGTACTCGTGCGTCGGCGTCTACCGGAACGGCCGTGTCGAGATCA
TCGCCAACGACCAGGGGAACCGGATCACGCCCTCGTGGGTCGCCTTCACCGACGGCGGCGAGCGGCTCATCGGCGAGGCC
GCCAAGAACCAGGCGGCGGCCAACCCGGAGCGGACCATCTACGACGCCAAGCGGCTCATCGGCCGGCAGTTCTCCGACGC
CGAGGTGCAGCGCGACATGAAGCTGCTGCCGTTCGCCGTCGTCGACCGGAACGGCAAGCCGCACGTGCGCGTCGAGGTGA
AGGACGGCGACGTGCGCGTGTTCAGCCCCGAGGAGGTGAGCGCCATGGTGCTCACGCGGATGAAGGAGACGGCCGAGGCC
TACCTCGGCGAGAAGGTCACGCGCGCCGTCGTCACCGTCCCGGCCTACTTCAACGACGCGCAGCGGCAGGCCACCAAGGA
CGCCGGCGTCATCGCCGGGCTCACCGTCGACCGCATCATCAACGAGCCCACCGCCGCCGCCATCGCCTACGGCATCGACA
AGAAGGGCGTGGAGAAGAACGTCCTCGTCTTCGACCTTGGCGGCGGCACGTTCGACGTCAGCATCCTCGCCATCGACAAC
GGCGTGTTCGAGGTCCTCGCCACCAACGGCGACACCCACCTCGGCGGCGAGGACTTCGACCAACGCCTCATGGACCACTT
CGTCAAGGTCATCCGCCGGAAGCACGGGCGCGACATCGCCGGCGACGCGCGCGCGCTGGGTAAGCTCCGCCGCGAGTGCG
AGCGCGCCAAGCGCGCGCTCAGCAACCAGCACCAGGTGCGCGTCGAGATCGAGTCCCTGTTCGACGGCGTCGACTTGTCG
GAGCCGCTCTCCCGGGCGCGGTTCGAGGAGCTCAACAGCGACCTCTTCAAGAAGACGATGGTGCCGGTGAGGAAGGCCAT
GGCGGACGCCGGGCTGGGCAAGGGCGACATCGACGAGATCGTCCTCGTCGGCGGCAGCACCAGGATCCCCAAGGTGCAGC
AGCTGCTCAAGGACTACTTCGGTGGCAAGGAGCCCAACCGCGGCGTCAACCCCGACGAGGCCGTGGCGTACGGCGCCGCC
GTGCAGGCCAGCATCATCAGCGGCCACGTCGACGAGAACACGGAGAGCATGATCCTCCTCGACGTCGCGCCGCTCACCCT
CGGCCTGGAGACGGCCGGCGGCGTGATGACCAAGCTGATCCCGCGCAACACGGTGGTGCCGACGAAGAAGACGCAGGTGT
TCACCACGTACAAGGACAAGCAGACGACGGTGACCATCCAGGTGTTCGAGGGCGAGCGGAGCATGACGAGGGACAACCGG
CTGCTCGGCAAGTTCGACCTCACCGGCATCGCGCCGGCGCCGAGGGGGGCGCCGCAGATCGAGGTGACGTTCGAGGTGGA
CGCGAACGGCATCCTCAGCGTGCTGGCCGCCGACAAGGCCACCGGCAGGTCGGAGAAGATCACCATCTCCGGCGACGACC
GCAAGATCAGCCAGGAGGAGATCGACCGGATGGTGCGCGAGGCGGAGGAGTTCGCCGAGGAGGACCGCCGGCACAGGGAG
CAGGTGGACGCCCGGAACAGCCTGGAGGCGTACGTCTACAACGTCAAGAGCACGCTCGGCGGCAAGATGGCGGACGCCAT
GGAGGGGGAGGAGAAGGAGAAGGTGGAGGAGGCGGTGAGGGAGGCGCACGAGTGGCTGGACGGCAACCCGGACGCCGGCA
AGGAGGAGTACGAGGAGAAGCTGCGGGAGCTGGAGGACGTGTGCAACCCCGTCATGTCGGCGGTGTACCAGAGGTCCGGC
GGCGGCGGCGGCGCACCGGAAGATGGCAACGTCGACGACGAGGATGACCACGATGAGCTTTAG

Alignment

ORF - retro_olon_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.52 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTVIGIDLGTTYSCVGVYKNGHVEIIANDQGNRITPSWVAFTDS-ERLIGEAAKNQAAVNPERTIFDVKR
          GTVIGIDLGTTYSCVGVY.NG.VEIIANDQGNRITPSWVAFTD..ERLIGEAAKNQAA.NPERTI.D.KR
Retrocopy GTVIGIDLGTTYSCVGVYRNGRVEIIANDQGNRITPSWVAFTDGGERLIGEAAKNQAAANPERTIYDAKR

Parental  LIGRKFEDKEVQRDMKLVPYKIVNKDGKPYIQVKIKDGENKVFSPEEVSAMILGKMKETAEAYLGKKIND
          LIGR.F.D.EVQRDMKL.P...V...GKP...V..KDG...VFSPEEVSAM.L..MKETAEAYLG.K...
Retrocopy LIGRQFSDAEVQRDMKLLPFAVVDRNGKPHVRVEVKDGDVRVFSPEEVSAMVLTRMKETAEAYLGEKVTR

Parental  AVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDLGGGTFDVSILTI
          AVVTVPAYFNDAQRQATKDAGVIAGL.V.RIINEPTAAAIAYG.DKKG.EKN.LVFDLGGGTFDVSIL.I
Retrocopy AVVTVPAYFNDAQRQATKDAGVIAGLTVDRIINEPTAAAIAYGIDKKGVEKNVLVFDLGGGTFDVSILAI

Parental  DNGVFEVLATNGDTHLGGEDFDQRIMEYFIKLIKKKYSKDISKDNRALGKLRREAERAKRALSNQHQVRV
          DNGVFEVLATNGDTHLGGEDFDQR.M..F.K.I..K...DI..D.RALGKLRRE.ERAKRALSNQHQVRV
Retrocopy DNGVFEVLATNGDTHLGGEDFDQRLMDHFVKVIRRKHGRDIAGDARALGKLRRECERAKRALSNQHQVRV

Parental  EIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMDDAGLEKSQIHEIVLVGGSTRIPKVQQLLRD
          EIESLFDG.D.SEPL.RARFEELN.DLF.KTM.PV.KAM.DAGL.K..I.EIVLVGGSTRIPKVQQLL.D
Retrocopy EIESLFDGVDLSEPLSRARFEELNSDLFKKTMVPVRKAMADAGLGKGDIDEIVLVGGSTRIPKVQQLLKD

Parental  YFEGKEPNKGVNPDEAVAYGAAVQGSILSGEGGDETKDILLLDVAPLTLGIETVGGVMTKLIPRNTVIPT
          YF.GKEPN.GVNPDEAVAYGAAVQ.SI.SG.....T....LLDVAPLTLG.ET.GGVMTKLIPRNTV.PT
Retrocopy YFGGKEPNRGVNPDEAVAYGAAVQASIISGHVDENTESMILLDVAPLTLGLETAGGVMTKLIPRNTVVPT

Parental  KKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPAAPRGTPQIEVTFEVDANGILNVKAED
          KK.QVFTTY.D.QTTV.IQVFEGERSMT.D.RLLGKFDL.GI..APRG.PQIEVTFEVDANGIL.V.A.D
Retrocopy KKTQVFTTYKDKQTTVTIQVFEGERSMTRDNRLLGKFDLTGIAPAPRGAPQIEVTFEVDANGILSVLAAD

Parental  KGTGKSEKITITNEKGRLSQEEIDRMVREAEEFAEEDKKVKERIDARNQLETYVYNMKNTVGDKDKLADK
          K.TG.SEKITI.......SQEEIDRMVREAEEFAEED....E..DARN.LE.YVYN.K.T.G...K.AD.
Retrocopy KATGRSEKITISGDDRKISQEEIDRMVREAEEFAEEDRRHREQVDARNSLEAYVYNVKSTLG--GKMADA

Parental  LESEEKEKVEAALKEALEWLDENQTAEKEEYEEKLKEVEAVCNPIISAVYQRTGGAPGGGADGEGGVDDE
          .E.EEKEKVE.A..EA.EWLD.N..A.KEEYEEKL.E.E.VCNP..SAVYQR.GG..GGGA...G.VDDE
Retrocopy MEGEEKEKVEEAVREAHEWLDGNPDAGKEEYEEKLRELEDVCNPVMSAVYQRSGG--GGGAPEDGNVDDE

Parental  --HDEL
          ..HDEL
Retrocopy DDHDEL

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_13 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G01477	1 retrocopy	retro_bdis_30,
Aegilops tauschii	F775_27431	1 retrocopy	retro_atau_11,
Oryza longistaminata	KN538684.1_FG046	1 retrocopy	retro_olon_13 ,
Hordeum vulgare	MLOC_55999	1 retrocopy	retro_hvul_1,
Oryza nivara	ONIVA01G37420	1 retrocopy	retro_oniv_8,
Oryza rufipogon	ORUFI02G01160	1 retrocopy	retro_oruf_18,
Sorghum bicolor	Sb04g001140	1 retrocopy	retro_sbic_39,
Triticum aestivum	Traes_6DS_A593093E1	1 retrocopy	retro_taes_72,