RetrogeneDB ID: retro_lper_7

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 6:13052157..13053972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR06G14510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR12G15690
• Aliases: None
• Description: None

Sequence

>retro_lper_7
ATGGCGGCGGCGGCGGCGGAGATTGGGGGAGACGATGGGGTGCGGCGGCGGCGGCGGTACTGGAGGTGGAGCAAGGCGGA
CTTCTTCCCGGAGCCGTCGTTCGCCAGCTGGCGTTCGTACGGCGGCGCGCTGGCCGCCACCGTGCCGCGGCTGGCCGACC
GCGTGGGGAGCCGCTCGTCGGAGGCGGTGGAGGCCGGCACGCTGCTCGCCCAGAGCGAGAACCCGCTGCGCCGCTGCCTG
TCGTGGATCGACCTCGCGCTCCTCGGATTCGGCTCCGTCGTCGGCTCCGGCGTCTTCGTCCTCACCGGCCAGGAGGCCCG
CTTCGACGCCGGCCCGGCGATCCCGCTCGCCTACGCCGCGGCGGGATTCTCCGCGCTGCTGTCGTCGTTCTGCTACGCCG
AGCTCGCCACCGAGATCCCATCCGCGGGTGGGTCCTTCTCCTACCTCCGCGTCGAGCTCGGCGACATCGCGGCTTTCCTC
GCCGCCGGGAACATCCTCCTCGAGGCCGTCGTCGGCGCGGCGGGGCTCGGCCGGTCATGGACGTCCTACCTCACCGCGCT
CCTCGGCAAGAGCGACACCGACGCGCTCCGCATCCACGTCCCAGCCCTCGCGGAGGGATTCAATCTGCTCGATCCGATCG
CCGTCGTCGTGCTCATCACCACCTCCGCCGTGGCGATGTCGGGCGCGCGGCTCACCTCCACGCTCAACTCGGTGGCTTCG
GTGGTGGGGATCGCCATCATCGCGTTCGTCCTCGCCGCGGGATTCTCCCACTTCGACGCGTCCAACCTCACGACCCCATC
CTTCTTCCCGTTCGGCGCCGCAGGCGTGTTCCGCGCGGCCGGGGTCGTGTACTGGTCCTACACGGGATTCGACATGGTGG
CGACGATGGCGGAAGAAACCAAAAACCCAGGCCGCGACATCCCACTAGGGCTCATCACGTCCATGTCATCCATCACCGTG
GTCTACTGCCTCATGTCACTGGCGCTGGTGGGGATGCAGCATTACAGCGAGATCGACGCGAACGCGGCGTACTCGGTGGC
GTTCGCGGCGGCGGGGATGAGGTGGGCGCGGTACGTGGTGGCGCTCGGCGCGCTCAAGGGGATGACGAGCGGGCTCCTGG
TCGGCGCGCTGGGGCAGGCGCGGTACACGACGCAGATCGCGAGGACGCACATGATCCCGCCCTACTTCGCGCTCGTCCAC
CCGGGCACGGGAACGCCCATCTACGCCACCGTCGCCGTCACGCTCGGCGCCGCCTGCGTCGCGCTCTTCTCCAGCCTCGA
CGTGCTCGCCTCCGTCTCCTCCATCAGCACGCTCTTCATCTTCGCGCTCGTCGCCGTCGCGCTCCTCGTCCGCCGGTACT
ACGTGTCCGGCGCCACGTCGCCGGCCCAGCTGCGCACGTTCCTCGCGTTCCTCGCGCTCGTCGTGCTCTCGTCGATCGGG
CTCTCGGTGTACTACAATTCGGGGTACGGTAGTCGGTGGCCGGGGTATGTTGGGTTCGGAGGAGGGTGGGCGGTCGGGGC
GGCGGGGCTGGCGGTGTTCGCGAAGCAGCAGAGGGTGCCCAAGGTGTACGGCGTGCCGCTCATGCCGTGGCTGCCGGCGA
TGTCGGTCGCCACCAACGTGTTCCTGATGGGGTCGCTCGGCACGGCGGCGTACGTGCGGTTCGGCATCTGCACGGCCGTC
ATGCTCGCCTACTACGTGCTCTTCGGCGTGCACGCCACCTACGACGTCGCGCACTCGGAGGACGCGGCGGCGGACAGCCT
CGAGCACGGCAAGATCGCGCCCGCGCCAGCGCCGCCGCCGCCGGCGCCGGCGTGA

Alignment

ORF - retro_lper_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.83 %
• Parental protein coverage: 96.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRGESKFFPEESFVSWGAYGRALMETGPRLRDRITARSADAVEIHEVKGRSGAEMRRSLTWWDLAWFGVG
          R.....FFPE.SF.SW..YG.AL..T.PRL.DR...RS..AVE.......S....RR.L.W.DLA..G.G
Retrocopy RWSKADFFPEPSFASWRSYGGALAATVPRLADRVGSRSSEAVEAGTLLAQSENPLRRCLSWIDLALLGFG

Parental  AVIGAGIFVLTGQEAKEAAGPAVVVSYAVSGVSAMLSVFCYTEFAIEIPVAGGSFAYLRVELGDFMAFIA
          .V.G.G.FVLTGQEA...AGPA....YA..G.SA.LS.FCY.E.A.EIP.AGGSF.YLRVELGD..AF.A
Retrocopy SVVGSGVFVLTGQEARFDAGPAIPLAYAAAGFSALLSSFCYAELATEIPSAGGSFSYLRVELGDIAAFLA

Parental  AGNILLEYCIGGAAVARSWTSYFATLLNHNPND-FRIHAAALSADYSRLDPIAVAVIAAICLLAVLSTKG
          AGNILLE...G.A...RSWTSY...LL.....D..RIH..AL......LDPIAV.V.......A......
Retrocopy AGNILLEAVVGAAGLGRSWTSYLTALLGKSDTDALRIHVPALAEGFNLLDPIAVVVLITTSAVAMSGARL

Parental  SSRFNYILSILHVVVLAFIIGAGLSKANIHNLTD-DFSPFGARGVFAASAVLFFAYIGFDAVSTMAEETK
          .S..N...S.......AF...AG.S.....NLT...F.PFGA.GVF.A..V....Y.GFD.V.TMAEETK
Retrocopy TSTLNSVASVVGIAIIAFVLAAGFSHFDASNLTTPSFFPFGAAGVFRAAGVVYWSYTGFDMVATMAEETK

Parental  NPARDIPIGLVGAMAVTTAVYCVLALTLCLMQPYREIDADAPFSVAFTAVGMDWAKYIVAFGALKGMTTV
          NP.RDIP.GL...M...T.VYC...L.L..MQ.Y.EIDA.A..SVAF.A.GM.WA.Y.VA.GALKGMT..
Retrocopy NPGRDIPLGLITSMSSITVVYCLMSLALVGMQHYSEIDANAAYSVAFAAAGMRWARYVVALGALKGMTSG

Parental  LLVSAVGQARYLTHIARTHMAPPFLAEVHPRLGTPVNATVAMMAATAIIALFTNLDILSNLLSISTLFIF
          LLV.A.GQARY.T.IARTHM.PP..A.VHP..GTP..ATVA.....A..ALF..LD.L....SISTLFIF
Retrocopy LLVGALGQARYTTQIARTHMIPPYFALVHPGTGTPIYATVAVTLGAACVALFSSLDVLASVSSISTLFIF

Parental  MLVALALLVRRYYLSGETTSSDRNKLAACLAVILSSAVATAAYWGLSGDGSRWAAYAVTVPAWIAATLCL
          .LVA.ALLVRRYY.SG.T.........A.LA....S......Y...SG.GSRW..Y......W......L
Retrocopy ALVAVALLVRRYYVSGATSPAQLRTFLAFLALVVLSSIGLSVYYN-SGYGSRWPGYVGFGGGWAVGAAGL

Parental  QIFVPAARSPEKWGVPMVPWLPSASIFINIFLLGSIDGKSFMRFGIWTAALLAYYFLVGLHASYDTAKAI
          ..F....R.P...GVP..PWLP..S...N.FL.GS.......RFGI.TA..LAYY.L.G.HA.YD.A...
Retrocopy AVFAKQQRVPKVYGVPLMPWLPAMSVATNVFLMGSLGTAAYVRFGICTAVMLAYYVLFGVHATYDVAH--

Parental  AAEAAACKVEEGK
          ...AAA...E.GK
Retrocopy SEDAAADSLEHGK

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_7 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
Leersia perrieri	LPERR12G15690	1 retrocopy	retro_lper_7 ,
Prunus persica	PRUPE_ppa003107mg	1 retrocopy	retro_pper_6,
Solanum lycopersicum	Solyc12g096380.1	1 retrocopy	retro_slyc_31,