RetrogeneDB ID: retro_lper_19

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 9:7602327..7603806(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR09G05840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR01G26100
• Aliases: None
• Description: None

Sequence

>retro_lper_19
ATGGCGGCATTGGCGAAGAAGCGGCCGGCGCGTCACCGCACACGTGCGACGCCGTCATCATCGTCGTCGTCGGATGTAGA
GGCGGCGAAGCGAGTGGTGTCCGATCTCAGAGACGCGTGCGCGACGCCGGCGACGACGCTGGACGCGGTGGCGGCGGCGA
TGGTGGGGGAAATGGACGCGGGGCTTGCGGCGGAGGGAGGCAGCAGCAAGGTGAAGATGATCGTCACCTTCGTCGACGCC
CTCCCAAACGGCGGCGAGGAGGGTTCGTTCTACGCGCTCGACCTCGGTGGCACAAACTTCCGCGTCCTCCGCGTTCGCCT
CGCCGGCGGCGGCGGAGTAGCGGAGCGCGTGGCGAGGGAGGTCCCGATCCCTCACCGCCTCATGTCCGGCGACGACGCGA
CGTCGGAGAATCTCTTTGATTTCATTGCTTCCGCGCTCGCGGAGTTCGTCGCCGACGAGGAAGGGCGTGACGGCGATGGC
GGCGATGGCGAGCGGATGAGGGAGCTCGGGTTCACCTTCTCGTTCCCCGTGCGGCAGACGTCGATCGCGTCGGGGAAGCT
GATACGGTGGACGAAGGCGTTCGCCGTCGACGACGCCGTCGGCGAGGACGTCGTGGCGGCGCTGCAGGCGGCGATGTCCA
AACACGGCCTCCACAACATGCGCGTGTCGGCGCTCATCAACGACACGGTCGGAACGCTCGCCACGGGATCATACTACGAC
GACGACACCGTCGCCGCCGTCATCCTCGGCACCGGCACGAACGCCGCGTACATCGAGAGCACGAACGCTATCGCCAAGCT
GTCTTCACCTCCGGCCGAGCTAGGCAATTCGTCGAACACCATGGTGATCAACACCGAGTGGGGAGGGTTCGACTCGCCAT
TCCTCCCGACCACCGAGTACGACCAAGCACTCGACGCCGAGAGCCTCAACCCCGGCGAGCAAACCTACGAGAAGCTCATC
TCCGGCCTCTACCTCGGCGACATCGTACGCCGAGTCCTCCTCAAAATCTCCACCAAATCCTCCCTCCTCGGCGGCGGCGA
CACCGATCTGCTCACAACCCGATTCGTCCTCACGACGCCCGACGTCTCATCGATGCACCACGACGAGACACCCGATCTCG
CCATCGTCGCCGACAAGCTCGCGGAGAAGCTCAACATCAGGGGCACGTCGCTGGAGACGAGGAGGATGGTCGTCGAGATC
TGCGACATCGTCGCCACGAGGTCCGCGCGGCTGGCCGCGGCAGGGATCGTGGGGATTCTGAGGAAGATCGGGAGAGGCGG
CGCTGGGGATGAGCGGAGATCGGTCGTCGCCGTCGACGGCGGGTTGTTCGAACACTACGCCAAATTCCGGCAATGTATGG
AGAGCACATTGGAGGAGATGCTTGGAGAGGAGGCAGCGGCAAGGATGTTTATCAAGCTCGCGAATGATGGGTCAGGCCTT
GGAGCTGCCCTGGTTGCAGCTGCTTACTCTCAGAGCTGA

Alignment

ORF - retro_lper_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.45 %
• Parental protein coverage: 94.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRRRSKREAEAERRSRAGAVIEEVEQRFSTPTALLRGIADAMVEEMERGLRADP-HAPLKMLISYVDNLP
          R.R.............A..V.........TP...L...A.AMV.EM..GL.A.......KM....VD.LP
Retrocopy RTRATPSSSSSSDVEAAKRVVSDLRDACATPATTLDAVAAAMVGEMDAGLAAEGGSSKVKMIVTFVDALP

Parental  TGDEQGLFYALDLGGTNFRVIRVQLGGREKRVVTQQYEEVAIPPHLMVG---TSMELFDFIAAELESFVK
          .G.E.G.FYALDLGGTNFRV.RV.L.G....V......EV.IP..LM.G...TS..LFDFIA..L..FV.
Retrocopy NGGEEGSFYALDLGGTNFRVLRVRLAGGGG-VAERVAREVPIPHRLMSGDDATSENLFDFIASALAEFVA

Parental  TE-GEDFHLPEG-RQRELGFTFSFPVHQTSISSGTLIKWTKGFCINGTVGEDVVAELSRAMERQGL-DMK
          .E.G.D.....G.R.RELGFTFSFPV.QTSI.SG.LI.WTK.F.....VGEDVVA.L..AM...GL..M.
Retrocopy DEEGRDGDGGDGERMRELGFTFSFPVRQTSIASGKLIRWTKAFAVDDAVGEDVVAALQAAMSKHGLHNMR

Parental  VTALVNDTVGTLAGGRYVDNDVAAAVILGTGTNAAYVEDANAIPKWTGILPRSGN----MVINMEWGNFK
          V.AL.NDTVGTLA.G.Y.D.D..AAVILGTGTNAAY.E..NAI.K........GN....MVIN.EWG.F.
Retrocopy VSALINDTVGTLATGSYYDDDTVAAVILGTGTNAAYIESTNAIAKLSSPPAELGNSSNTMVINTEWGGFD

Parental  SERLPRSEYDSALDFESLNPGEQIYEKMISGMYLGEIVRRILLKLAHDASLFGDVVPPKLEQRFILRTPD
          S..LP..EYD.ALD.ESLNPGEQ.YEK.ISG.YLG.IVRR.LLK.....SL.G......L..RF.L.TPD
Retrocopy SPFLPTTEYDQALDAESLNPGEQTYEKLISGLYLGDIVRRVLLKISTKSSLLGGGDTDLLTTRFVLTTPD

Parental  MSAMHHDTSHDLKHLGAKLKDILGVADTSLEARYITLHVCDIVAERGARLAAAGIYGILKKLGRDKVPSD
          .S.MHHD...DL.....KL...L....TSLE.R......CDIVA.R.ARLAAAGI.GIL.K.GR......
Retrocopy VSSMHHDETPDLAIVADKLAEKLNIRGTSLETRRMVVEICDIVATRSARLAAAGIVGILRKIGRG---GA

Parental  GSKQRTVVALDGGLYEHYKKFRTCLEATLADLLGDEAASSVVVKLANDGSGIGAALLAASHSQ
          G...R.VVA.DGGL.EHY.KFR.C.E.TL...LG.EAA.....KLANDGSG.GAAL.AA..SQ
Retrocopy GDERRSVVAVDGGLFEHYAKFRQCMESTLEEMLGEEAAARMFIKLANDGSGLGAALVAAAYSQ

Legend:

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

Expression

RNA-Seq

Leersia perrieri was not studied using RNA-Seq expression data.

ChIP-Seq

Leersia perrieri was not studied using ChIP-Seq data.

EST

Leersia perrieri was not studied using EST data.

TSS

Leersia perrieri was not studied using FANTOM5 data.

Lab

retro_lper_19 was not experimentally validated.

Homology

Retrocopy orthology:

Leersia perrieri 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,