RetrogeneDB ID: retro_osat_8

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 7:15293214..15294711(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS07G0446800
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0742500
• Aliases: None
• Description: None

Sequence

>retro_osat_8
ATGGCGGCGGCGGCGGTGGCGGCAGATCAGAAGGTGGTGACGATGACGAGCCTCCGGGAGGGCTGCGCTTGCGCGGCGCC
TCCTGCTGCAGCTGCGCCGCCGATGCCGAAGATGGCGGCGGCGCAGAGGGTGGTGGCGGAGCTGAGAGAAGCGTGCGCGA
CGCCGGCGGCGAGGCTGGCGGAGGTGGCCGCGGCGATGGCCGGCGAGATGGAGGCCGGGCTGGCGGTGGAGGGCGGCAGC
AGCGAGATGAAGATGATCGTGTCGTACGTCGACAGCCTCCCCACCGGCGGCGAGGAGGGGTCGTACTACGCGCTCGACCT
CGGCGGCACCAACTTCCGCGTCCTCCGCGTGCGGCTTGCCGGCGGCGGCGTCGCCGAGCGCGTGGCGAGGGAGGTCCCGA
TCCCTCCCGGCCTCATGTCCGGCGGCGGCGCCACCTCGGAGTGCCTCTTCGGCTTCATCGCCTCCGCGCTAGCCGAGTTC
GTCGGCGAGGAGGAAGAAGAAGGCGGCCTCGACGGCGGCGAGAGGGAGCTTGGGTTCACCTTCTCCTTCCCCGTGCACCA
AACCTCCATCGCGTCGGGGACGCTCATCCGGTGGACGAAGGCGTTCGCCGTCGACGACGCGATCGGCGAGGACGTCGTGG
CGGCGCTGCAGGCGGCCATGTCGGAGCGGGGGCTCGACATGCGCGTGTCGGCGCTCATCAACGACACCGTCGGGACGCTC
GCCGCGGGCAGCTACTACGACGAGGACGTCGTGGCCGCCGTCATCCTCGGCACCGGCACGAACGCCGCCTACGTCGAGGA
CGCCACCGCCATCGCCAAGCTACACCCATCGCAGCTGCCAGCATCGAACACCATGGTGATCAACACCGAGTGGGGCAGCT
TCGCCTCGCCGTGCCTCCCATTGACGGAGTTCGACGAAGCACTCGATCAGGAGAGCCTCAACCCCGGCGAGCAGACCTAC
GAGAAGCTCATCTCCGGGATGTACCTCGGCGAGATCGTCAGGAGGGTCCTCCTCAAGATCTCCTCCCGGTGCCCCTCCCT
CCTCGGCGGCGCCGGCGAGCTCGCGACGCCGTTCGTCCTCAGGACACCCGACGTGTCCGCGATGCACCACGACGAGACGC
CCGACCTGAGCATCGTCGGCGAGAAGCTGGAACGCACGCTGGGCATCCGCGGCACGTCGCCGGAGGCGAGGAGGATGGTC
GTCGAGGTGTGCGACATCGTCGCCACGAGGGCCGCCCGGCTGGCCGCGGCGGGGATCGTCGGGATCCTGAAGAAGATCGG
GAGGGTCGACGGCGGCGAGGGGCGGAGGAGGAGGTCGGTGGTCGCCGTGGACGGCGGGCTGTTCGAGCACTACGGCAAGT
TCCGGCGGTGCATGGAGAGCGCGGTGAGGGAGCTGCTCGGAGAGGCGGCGGCGGAGAGGGTGGTCGTCAAGCTCGCCAGC
GACGGCTCCGGGCTCGGCGCCGCCCTGGTTGCAGCTGCTCACTCGCAGAGAGCATAA

Alignment

ORF - retro_osat_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.92 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAVIEEVEQRFSTPTALLRGIADAMVEEMERGLRADP-HAPLKMLISYVDNLPTGDEHGLFYALDLGGT
          A..V..E......TP.A.L...A.AM..EME.GL.........KM..SYVD.LPTG.E.G..YALDLGGT
Retrocopy AQRVVAELREACATPAARLAEVAAAMAGEMEAGLAVEGGSSEMKMIVSYVDSLPTGGEEGSYYALDLGGT

Parental  NFRVIRVQLGGREKRVVSQQYEEVAIPPHLMVG---TSMELFDFIAAELESFVKTEGEDFHLPEGRQREL
          NFRV.RV.L.G....V......EV.IPP.LM.G...TS..LF.FIA..L..FV..E.E...L..G..REL
Retrocopy NFRVLRVRLAGGG--VAERVAREVPIPPGLMSGGGATSECLFGFIASALAEFVGEEEEEGGL-DGGEREL

Parental  GFTFSFPVHQTSISSGTLIKWTKGFSINGTVGEDVVAELSRAMERQGLDMKVTALVNDTVGTLAGGRYVD
          GFTFSFPVHQTSI.SGTLI.WTK.F......GEDVVA.L..AM...GLDM.V.AL.NDTVGTLA.G.Y.D
Retrocopy GFTFSFPVHQTSIASGTLIRWTKAFAVDDAIGEDVVAALQAAMSERGLDMRVSALINDTVGTLAAGSYYD

Parental  NDVAAAVILGTGTNAAYVEHANAIPK-WTGLLPRSGNMVINMEWGNFKSERLPRSDYDNALDFESLNPGE
          .DV.AAVILGTGTNAAYVE.A.AI.K.....LP.S..MVIN.EWG.F.S..LP....D.ALD.ESLNPGE
Retrocopy EDVVAAVILGTGTNAAYVEDATAIAKLHPSQLPASNTMVINTEWGSFASPCLPLTEFDEALDQESLNPGE

Parental  QIYEKMISGMYLGEIVRRILLKLAHDA-SLFGDVVPTKLEQRFILRTPDMSAMHHDTSHDLKHLGAKLKD
          Q.YEK.ISGMYLGEIVRR.LLK......SL.G......L...F.LRTPD.SAMHHD...DL...G.KL..
Retrocopy QTYEKLISGMYLGEIVRRVLLKISSRCPSLLGGA--GELATPFVLRTPDVSAMHHDETPDLSIVGEKLER

Parental  ILGVADTSLEARYITLHVCDLVAERGARLAAAGIYGILKKLGRDRVPSDGSQKQRTVIALDGGLYEHYKK
          .LG...TS.EAR.....VCD.VA.R.ARLAAAGI.GILKK.G..RV........R.V.A.DGGL.EHY.K
Retrocopy TLGIRGTSPEARRMVVEVCDIVATRAARLAAAGIVGILKKIG--RVDGGEGRRRRSVVAVDGGLFEHYGK

Parental  FRTCLEATLADLLGEEAASSVVVKLANDGSGIGAALLAASHSQYA
          FR.C.E.....LLGE.AA..VVVKLA.DGSG.GAAL.AA.HSQ.A
Retrocopy FRRCMESAVRELLGEAAAERVVVKLASDGSGLGAALVAAAHSQRA

Legend:

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

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_8 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 longistaminata	KN538775.1_FG004	1 retrocopy	retro_olon_14,
Leersia perrieri	LPERR01G26100	1 retrocopy	retro_lper_19,
Oryza sativa japonica	OS01G0742500	1 retrocopy	retro_osat_8 ,