RetrogeneDB ID: retro_lper_18

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 1:16400220..16401486(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR01G18490
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR04G11710
• Aliases: None
• Description: None

Sequence

>retro_lper_18
ATGGCAGAACAGAAGGTGACTCTCGCCGAGCCGCTGCTTCCGGCGAAGGAAGCCGACGACGACGTGGAGGCGCAGCTCAC
ATCCTACAACACCGGCGCCTCATTCTCCAGAACATGCCTCAACCTCACCAACGCCGTCTCCGGCATCGGGGTGCTGTCCA
TGCCGTACGCCGTGTCGCAGGGCGGGTGGCTCAGCCTCCTCCTCTTCGTGGCCGTCGGCGCCGTCTGCTACTACACCGGC
ACGCTCATCGAGCGCTGCATGCGCGCAGACGGCTCGATCGCCAGCTACCCGGACATCGGCCAGTTCGCGTTCGGCGACGC
GGGGCGGAGGGCTATCGCCTTCTTCATGTACGTCGAGCTCTACCTCGTCGCCATCAGCTTCCTCGTCCTCGAGGGCGACA
ACCTCGACAAGCTCTTCCCGGGCACGACCATGGAGCTCCTCGGGTACAAGCTCCACGGGAAACAGCTCTTCATCGTGCTC
GCCGCGGGCGTGATTCTCCCCACCACGTGGCTCAAGAACCTCGGCATGCTCGCCTACGTGTCGGCGGCCGGGCTCGTCGC
GTCGGCCGCCCTGACGGCGTCGCTCGTCTGGGCCGGCGTCGCCGAGACGGGATTCCACAAAACCAGCAACGTCATCAACC
TCGTGGGAATTCCAACCTCGCTTGGCCTCTACTTCGTGTGCTTCACCGGCCACGCCGTGTTCCCGACGATCTACTCCTCC
ATGAAGAGCAACAAGCACTTCTCCAAGGTTCTCCTCATCTCGTCGGTGCTCTGCAGCCTCAACTACGGGATCACGGCGGT
GCTCGGCTACCTCATCTACGGCGACGACGTGCAGTCGCAGGTGACGCTCAACCTGCCCGCGGGGAAGCTCTGCACCAAGG
TCGCCATCGTGATGACGCTGGTGAACCCGCTGGCCAAGTACGCGCTGCTCGTCGCGCCGATCACGGCGGCGGTCAAGGAG
AGGCTCGCGCTGGGGCAGCGAGGCGGCGCGCCGGCGAGGGTGGCCATCAGCACAGCCGTGCTCGCCAGCACGGTGGTGGT
GGCGTCGACGGTGCCGTTCTTCGGATACCTCATGTCGTTCATCGGGTCGTTTCTTAGTGTTATGGCGACCGTGCTGTTCC
CCTGCCTCTGTTACCTCAAGATCTACAAGGCCGACGGTATCCGCCGCACGGAGCTGGTGGCGATCGCCGGAATTCTGATG
CTTGGGGTGTTCGTCGCCGTCACCGGCACGTACACTTCTCTCCAGCAGATTATAGGCACTTTCTGA

Alignment

ORF - retro_lper_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.43 %
• Parental protein coverage: 89.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERDHEAQRSPDADDDGATFVRTCFNGLNALSGVGLLSIPYALSEGGWLSLVLLLAVAMVCCYTGVLLRRC
          E.D............GA.F.RTC.N..NA.SG.G.LS.PYA.S.GGWLSL.L..AV..VC.YTG.L..RC
Retrocopy EADDDVEAQLTSYNTGASFSRTCLNLTNAVSGIGVLSMPYAVSQGGWLSLLLFVAVGAVCYYTGTLIERC

Parental  MAASPSVRGYPDIGALAFGAKGRLAVSAFLYAELYLVAIGFLILEGDNLDKLFPGTSLSFGDVVVSGKQL
          M.A..S...YPDIG..AFG..GR.A...F.Y.ELYLVAI.FL.LEGDNLDKLFPGT..........GKQL
Retrocopy MRADGSIASYPDIGQFAFGDAGRRAIAFFMYVELYLVAISFLVLEGDNLDKLFPGTTMELLGYKLHGKQL

Parental  FVVLVAVVILPTTWLRSLAVLAYVSASGVLASVVVVFCVLWAAVGDGVGFQGKGRMLNVSGLPTALGLYT
          F.VL.A.VILPTTWL..L..LAYVSA.G..AS........WA.V....GF.......N..G.PT.LGLY.
Retrocopy FIVLAAGVILPTTWLKNLGMLAYVSAAGLVASAALTASLVWAGVAE-TGFHKTSNVINLVGIPTSLGLYF

Parental  FCYCGHAIFPTLCNSMKEKDKFSKVLVICFVACTLNYGSMAILGYLMYGDDVKSQVTLNLPEGKISSKLA
          .C..GHA.FPT...SMK....FSKVL.I..V.C.LNYG..A.LGYL.YGDDV.SQVTLNLP.GK...K.A
Retrocopy VCFTGHAVFPTIYSSMKSNKHFSKVLLISSVLCSLNYGITAVLGYLIYGDDVQSQVTLNLPAGKLCTKVA

Parental  IYTTLINPFSKYALMVTPVAQAIEERLLAGNK--RSVNILIRTLIVVSTVVIALTVPFFGHLMALVGSLL
          I..TL.NP..KYAL.V.P...A..ERL..G..........I.T....STVV.A.TVPFFG.LM...GS.L
Retrocopy IVMTLVNPLAKYALLVAPITAAVKERLALGQRGGAPARVAISTAVLASTVVVASTVPFFGYLMSFIGSFL

Parental  SVMASMLLPCICYLKIFGLARCGRGETLLIVTIIVLGSLVAATGTYSSLKKIIYEF
          SVMA..L.PC.CYLKI.......R.E...I..I..LG..VA.TGTY.SL..II..F
Retrocopy SVMATVLFPCLCYLKIYKADGIRRTELVAIAGILMLGVFVAVTGTYTSLQQIIGTF

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_18 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_07363	1 retrocopy	retro_atau_17,
Leersia perrieri	LPERR04G11710	1 retrocopy	retro_lper_18 ,