RetrogeneDB ID: retro_lper_1

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 6:8801551..8803978(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR06G11080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR03G03650
• Aliases: None
• Description: None

Sequence

>retro_lper_1
ATGGCGAGCCCGAGCTCCTCCGCCGCCGCCGCCGCCGCCGGCGACACGGAGAAGGATTACACGACGGCGATCCTGGAACG
CAAGAAATCCCCAAACCGGCTGATGGTCGACGAGGCGACCCACGACGACAACTCCATCATCGGAATACACCCGGACACCA
TGGACGCGCTCGACCTCCTCCGTGGCGACGTCGCCCTCCTCAAGGGCAAGAAGCGCAAGGACACGGTCGGCGTCGTCCTC
ATCGACGACACCTGCGACCCCACCAAAATCCGTATGAACAAGGTCGTCAGAAAAAACCTCGGCGTCCGCCTCGGCGACGT
GGTCTCCGTCCACCAACTCGCCAGCGTCAAGCACGCCACACGCGCGCACATCCTCCCCATCGACGACACGGTGGAGGGCA
TCTCCGGAAACCTCTTCGACGCGTTCTTGCAGCCATACTTCAGCGAAGCCTATCGCCCGCTGAGGAAAGGGGATCTCTTC
ATTGTCAGGGGAGTTGGGATGCGAAGCGTGGAGTTCAAGGTTGTGGAGATTGAGCCGGAGGAGTATTGCGTCGTGGCGCC
TGACACGGAGATTTTCTGTGACGGTGAGCCGATTAAGAGGGAGGATGAGGAGAGGCTTGATGATGTTGGGTACGACGATG
TTGGTGGTGTGAGGAATCAGATGGCGCAGATTAGGGAGCTGGTCGAGTTGCCATTGAGGCATCCGCAGTTGTTCAAGTCG
ATTGGTGTGAAGCCACCAAAGGGGATTTTACTGTACGGACCACCCGGGACGGGCAAAACTCTCATTGCACGAGCCGTCGC
TAATGAGACTGGGGCGTTCTTCTTCCTCATCAATGGGCCGGAGATCATGTCGAAGCTTGCTGGGGAGAGTGAGAGCAATC
TAAGGAAGGCGTTCGAGGAGGCGGAGAAGAACGCGCCGTCGATCATCTTCATCGACGAGATCGACTCGATCGCCCCCAAA
CGCGACAAGACGCACGGCGAGGTCGAGAGGAGGATCGTGTCGCAGCTGCTGACGCTCATGGATGGGCTCAAGGCGCGTGC
GCACGTGGTCGTCATGGGCGCCACGAATCGGCCCAACAGCATCGATCCTGCGCTCAGGAGGTTCGGAAGGTTCGATCGGG
AGATCGACATTGGTGTTCCTGACGAGGTTGGACGGCTCGAGGTTGTGGGGATTCACACCAAGAACATGAAGCTTTCTGAG
GATGTGAATCTTGAGATAATCGCCAAGGATACTCATGGGTATGTTGGTGCTGATCTTGCTGCTCTTTGCACTGAGGCTGC
TCTCCAATGCATCCGTGAGAAGATGGACATTATTGATCTTGAGGATGACACGATCGATGCTGAGATTCTTAATTCGATGG
CTGTCACGAATGATCATTTCAAGATTGCGTTGCAGACGAGCAACCCGTCTGCTCTTCGTGAAACCGTCGTCGAAGTCCCA
AATGTGTCATGGGAAGATGTGGGTGGATTGGAGAGTGTGAAACGGGAGCTGCAGGAGACCGTGCAGTATCCAGTGGAGCA
TCCGGAGAAATTCGTGCAGTTTGGAATGTCGCCGTCAAAGGGGGTTCTCTTCTATGGCCCTCCTGGCTGTGGCAAGACAT
TGTTAGCGAAGGCGATCGCGAACGAGTGCAAGGCAAATTTCATCAGCATCAAGGGACCCGAATTGCTTTCCAAGTGGTTT
GGTGAGAGTTCAGCCAATGTGCGCGAGGTTTTCGACAAGGCGAGACAGTCGGCTCCGTGTGTGTTGTTCTTCGATGAGCT
CGATTCGATTGCTACCCAGAGAGGAAGTAACATTGGTGATTCGGGTGCTGCTGATAGGGTTCTGAATCAGCTTCTGACTG
AGATGGATGGCATGAACGCCAAGAAGACAGTGTTCATCATCGGCGCGACTAATCGGCCGGATATCATCGATTCTGCCTTG
CTCAGGCCAGGCCGTCTCGATCAGCTCATCTACATTCCTCTCCCTGATGAGCAATCCAGGCTGCAGATCTTCAAATCTTG
CCTCAGGAAGTCACCTGTGGCAAACGATGTCAACCTGAATTCCCTTGCGAAATTCACCAACGGGTTCAGCGGTGCTGACA
TTACAGAGATCTGCCAGCGTGCGTGCAAGTACGCCATCAGGGAGGACATTGAAAAGGACATTGAGAAGGAGAAGAAGAGA
AAGGAGAACCCTGAAGCTGGAGAAGCCATGGAGGAGGATGATGACGAGGTGGCTGAGATCAAAGCTGCTCACTTCGAGGA
GTCGATGAAGTACGCTCGCAGGAGTGTGAGCGATGCCGACATCCGCAAGTACAATGCCTTCGCACAGACTCTGCAGCAGT
CTCGTGGATTTGGCACCCAGTTCAGGTTCGCTGATCACCCAGCTGCTTCTGGGGTAGCCGCTACTGCGGCAACTGCAGCT
GACGAGGAGGATGACCTTTATAATTAG

Alignment

ORF - retro_lper_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQGEPSSSDPKG--KKDYSTAILERKKSPNRLVVDEAANDDNSVIGMHPDTMERLQLFRGDTVLLKGK
          MAS..........G...KDY.TAILERKKSPNRL.VDEA..DDNS.IG.HPDTM..L.L.RGD..LLKGK
Retrocopy MASPSSSAAAAAAGDTEKDYTTAILERKKSPNRLMVDEATHDDNSIIGIHPDTMDALDLLRGDVALLKGK

Parental  KRKDTICIVLADDTCEEPKIRMNKVVRKNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTVEGITGNLFD
          KRKDT...VL.DDTC...KIRMNKVVRKNL.VRLGDVVSVHQ...VK...R.HILPIDDTVEGI.GNLFD
Retrocopy KRKDTVGVVLIDDTCDPTKIRMNKVVRKNLGVRLGDVVSVHQLASVKHATRAHILPIDDTVEGISGNLFD

Parental  AFLKPYFLEAYRPLRKGDLFLVRG-GMRSVEFKVIETDPAEYCIVAPDTEIFCDGEPIKREDEERLDEVG
          AFL.PYF.EAYRPLRKGDLF.VRG.GMRSVEFKV.E..P.EYC.VAPDTEIFCDGEPIKREDEERLD.VG
Retrocopy AFLQPYFSEAYRPLRKGDLFIVRGVGMRSVEFKVVEIEPEEYCVVAPDTEIFCDGEPIKREDEERLDDVG

Parental  YDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFLINGP
          YDDVGGVR.QMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPG.GKTLIARAVANETGAFFFLINGP
Retrocopy YDDVGGVRNQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGTGKTLIARAVANETGAFFFLINGP

Parental  EIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTHGEVERRIVSQLLTLMDGLKARAHVI
          EIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKR.KTHGEVERRIVSQLLTLMDGLKARAHV.
Retrocopy EIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKRDKTHGEVERRIVSQLLTLMDGLKARAHVV

Parental  VMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVDLELIARDTHGYVGADLA
          VMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEV..IHTKNMKL.EDV.LE.IA.DTHGYVGADLA
Retrocopy VMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVVGIHTKNMKLSEDVNLEIIAKDTHGYVGADLA

Parental  ALCTEGALQCIREKMDIIDLEDETIDAEILNSMAVTNDHFKTALGTSNPSALRETVVEVPNVSWEDIGGL
          ALCTE.ALQCIREKMDIIDLED.TIDAEILNSMAVTNDHFK.AL.TSNPSALRETVVEVPNVSWED.GGL
Retrocopy ALCTEAALQCIREKMDIIDLEDDTIDAEILNSMAVTNDHFKIALQTSNPSALRETVVEVPNVSWEDVGGL

Parental  ENVKRELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWF
          E.VKRELQETVQYPVEHPEKF..FGMSPSKGVLFYGPPGCGKTLLAKAIANEC.ANFIS.KGPELL..WF
Retrocopy ESVKRELQETVQYPVEHPEKFVQFGMSPSKGVLFYGPPGCGKTLLAKAIANECKANFISIKGPELLSKWF

Parental  GESEANVREIFDKARQSAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGA
          GES.ANVRE.FDKARQSAPCVLFFDELDSIATQRGS..GD..GAADRVLNQLLTEMDGMNAKKTVFIIGA
Retrocopy GESSANVREVFDKARQSAPCVLFFDELDSIATQRGSNIGDS-GAADRVLNQLLTEMDGMNAKKTVFIIGA

Parental  TNRPDIIDPALLRPGRLDQLIYIPLPDDQSRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADITEICQ
          TNRPDIID.ALLRPGRLDQLIYIPLPD.QSRLQIFK.CLRKSPVA.DV.LN.LAK.T.GFSGADITEICQ
Retrocopy TNRPDIIDSALLRPGRLDQLIYIPLPDEQSRLQIFKSCLRKSPVANDVNLNSLAKFTNGFSGADITEICQ

Parental  RACKYAIRENIEKDIEREKRRKDNPEAME--EDEADEIAEIKAAHFEESMKYARRSVSDADIRKYQAFAQ
          RACKYAIRE.IEKDIE.EK.RK.NPEA.E..E...DE.AEIKAAHFEESMKYARRSVSDADIRKY.AFAQ
Retrocopy RACKYAIREDIEKDIEKEKKRKENPEAGEAMEEDDDEVAEIKAAHFEESMKYARRSVSDADIRKYNAFAQ

Parental  TLQQSRGFGTEFRFADQPASGAGAAADPFSSAAAAADDDDLYS
          TLQQSRGFGT.FRFAD.PA....AA......A.AA...DDLY.
Retrocopy TLQQSRGFGTQFRFADHPAASGVAA----TAATAADEEDDLYN

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_1 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1 ,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g046840	1 retrocopy	retro_sbic_42,