RetrogeneDB ID: retro_lper_14

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 5:11759734..11762950(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR05G12020
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR08G09260
• Aliases: None
• Description: None

Sequence

>retro_lper_14
ATGGCGGCGAGCGACGGCCAGCTCAAGACCTGGGTCTCCGACCGCCTCATGGCTCTCGTGGGCTACTCCCAGGGCGTCGT
GGCGCAGTTCGTCGTCCGCCTCGCGCGGGATTGTGCCTCGGCGGGTGACCTCGCCGCCCGGCTCGTCGAAATCGGCGGGT
TCCCGTCCTCCCCCGACACCGTCGCCTTTGCGGAGGACATGTTCGGGAGGGTTCCCCGCAATGGCGGCGGCGGCGGCGAC
GGCGATGGGGTCAGCGAGTACCAGAGACAGGTGCAGGAGGCGGCTGCGGTTGCCAAGAAGCAGAGCACCTTCAAGCTGCT
CGACGACGAGGGCGGCGTCGATGCCGGAGTTTCCGCGTCGTCCTCCACCAGTGTCAGGAAGCGTTTCAGGAGGAAGGAGG
CCGTGATCGAAGACGATGAGGCGAGTGCGATGCACGATTCCGGACGGAACGTGCGACGGCGGTGTAGCCCGGAGGAGGAC
GGCGACGGCGACTCCGGCGAGGAGGAGGAGATGGATCGGGATCAGATCGAGAAGGCGCGGCTCGAGCGGAACATCAGGGA
GCGCGACGCGGCGAGCACGAGGAGGCCGATGGATCGGAAGCCGACGAAGCGAGAGCAGGACGAGCTTGCGCGCCGGTCGG
AAGCCATGGACCGGAACGACGACGCCTCGGAGCTCAGGAGGCTCTCGCGGCACGCGTACCTGCAGACGCGGAAGGAGAAG
AAGGTGGACGAGTTGCGCGACGAGATCGTCGACCACGAGTTCCTCTTCCCCGGCGGCTTCCAGCTGTCGGCCGCCGAGGA
GAGGGACATGCGGCGCAAGAAGGAAGTGTACGGCCTCGTGCAAGATCGCGACAAGAACAACGACGGCGCCGGCGACGATT
ATTATTACCGAATGCCGGAGGCATACGACGCCGCCGCGAACATCGATCAGGAGAAGAGATTCTCGGTGGCGCGGCGACGG
TACGAGGAGCCGGAGGCGAGGGACGGGAAGACGGCGAAGGCGTTCACCGAGCAGGAGGCATGGGAGGAGCAACAGATACG
GAAATCCATGCTGCAGCTCGGATCAACGGATCGTGGCCGGCGCGGCGACGAGTACGAGCTCCTGTTCGACGACGGCGTCG
AGTTCGTCAGGTCGTCGGTGATGGCAGGTACCGTGCCAGACGACGCCGAGGCCGCCATGGATGCCAAGGCGACATTGCAA
GACGAGAGGAAGACTCTCCCGGTGTACAAGCTCAAGGACGACCTGCTCAAGGCCATCGACGAGTACCAGGTTCTGATCAT
CGTCGGCGAGACCGGGTCAGGCAAGACGACGCAGATACCGCAGTACCTCCACGAGGCCGGGTACACGGCGAAGGGAAAAA
AGAAGGTGGCGTGCACGCAGCCGCGGCGCGTGGCGGCGATGAGCGTGGCGGCGCGTGTGGCCGAGGAGATGGGCGTCAAG
CTCGGCCACGAGGTCGGCTACTCCGTCAGGTTCGAGGACTGCACGTCTGACAAGACGGTGATCAAGTACATGACCGACGG
GATGCTCCTCCGCGAGTTCCTCGGCGAGCCCGACCTGGGCAGCTACAGCGTCGTCGTCATCGACGAGGCACACGAGCGGA
CGCTCTCCACCGACATCCTCTTCGGCCTCGTCAAGGACATCGCCCGGTTCCGTCCCGACCTGAAGCTGCTCATCTCCAGC
GCCACGCTCAACGCCGAAAAGTTCAGCGACTTCTTCGACTCAGCACCCATCTTCCGGATCCCCGGCCGGCGGTTCGACGT
GGCAGTGCACTACACCAAGGCGCCGGAGGCAGACTACATCGACGCCGCTATCGTGACGGTGCTGCAGCTGCACGTGACGG
AGCCGGCTGCCAGCGGCGACATTCTGCTGTTTCTCACCGGGCAGGAGGAGATCGAGACGGTGGAGGAGATACTGCGGCAG
CGGCTGAGGGTTCTCGGCGGCAAGGTGGCTGAGCTGGTGATCTGTCCCATCTACGCCAACCTCCCAACAGAGCTGCAGGC
CAAGATCTTCGAGCCGGCGCCGGAGGGCGCGCGCAAGGTGGTTCTCGCCACCAACATCGCCGAGACGTCGCTGACCATCG
ACGGGATCAAGTACGTGGTCGACCCGGGGTTCTGCAAGGTGAAGTCGTACAACCCGCGCACCGGGATGGAGTCGCTGCTC
GTTGCGCCGGTGTCCAAGGCGTCGGCGGAGCAGCGGGCCGGACGGTCGGGGCGCACCGGGCCGGGCAAGTGCTTCCGGCT
CTACACGGAGTACAACTTCCTCAACGACCTCGACGCCGACACGGTCCCCGAGATCCAGCGGAGCAACCTGGCCAACGTCG
TGCTCGCGCTCAAGACGCTTGGGATCAACGACCTCGTGGGGTTCGACTTCATGGACCCGCCGGCGGCGGAGTCGCTGCTC
AAGGCCCTGGAGGAGCTCTTCGCCCTCGGCGCGCTCAACAGCCGCGGCGAGCTCACCAAGACAGGGAGGAGGATGGCGGA
GTTCCCGCTTGACCCCATGCTCTCCAAGGCCATCGTCGCGTCGGAGAAGTACGGGTGCTCGGAGGAGGTGATCACCATCG
CGGCCATGCTGTCCGCGGGCAACGCCGTGTTCTACCGTCCAAAGGACAAGCAGGTCCACGCCGACGCGGCGCGGCGGGCG
TTCCACGCCGCCGGCAACGTGGGCGACCACGTCGCGCTGCTCAACGTGTACAACGCGTGGAGGGAGTCGGGCTACTCGGC
GCAGTGGTGCCGAGAGAGCTTCGTGCAGCACCGCACCATGCGGCGGGCGCGGGACGTGCGTGGCCAGCTGGTGGCGCTCC
TGGAGCGGGTGGAGATCGCGCCGTGCTCCGCCGCCGGAGACCTCGGCGCCGTCAGGAAGGCGATCACGGCGGGGTACTTC
CGCCACGCCGCGCGGCTGCAGAGGGACGGGTCGTACCGCGCCGTCAAGAGCAGGCAGACGGTGTTCGTCCACCCGAGCTC
CGGGGTGGCGCAGGCGCCGCCGCGGTGGGTGGTGTACCACGAGCTGGTGCTCACGACCAAGGAGTACATGCGGCAGGTGA
CGGAGCTCAAGCCGGAGTGGCTGGTGGAGATTGCGCCGCACTACTACGAGCGCAAGGACGTCGACGAGCCTGAGGTCAAG
AAGATGACGTCGACGGCCACGGGGCAAGAGAAGACGACGACCGGAGCTACACCCACGAAGCATACTCCAAATCTTAATAG
TTTCTTCGACGTATAA

Alignment

ORF - retro_lper_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.45 %
• Parental protein coverage: 82.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASTSSKSRKHFRRKAEDQDDGNDDDETTKQ-DFGRNVKRRTEDMDDEDGGNDTDEEQERIRDQQERAQLE
          A..S..S....R...........DDE.....D.GRNV.RR......EDG..D..EE.E..RDQ.E.A.LE
Retrocopy AGVSASSSTSVRKRFRRKEAVIEDDEASAMHDSGRNVRRRCSP--EEDGDGDSGEEEEMDRDQIEKARLE

Parental  KNMRERDAANTRKLMERQLSKEEQEEIIRRSQAVDKN-DTSDLRKFSRQAYLQKRRDKKIDEIRDEILDH
          .N.RERDAA.TR..M.R...K.EQ.E..RRS.A.D.N.D.S.LR..SR.AYLQ.R..KK.DE.RDEI.DH
Retrocopy RNIRERDAASTRRPMDRKPTKREQDELARRSEAMDRNDDASELRRLSRHAYLQTRKEKKVDELRDEIVDH

Parental  EYIFQ-DVKLTEAEEKEFRYKKKIYDLVKEHVESADDVAE---YKMPEAYDMGESVNQEKRFSVAMQRYK
          E..F.....L..AEE...R.KK..Y.LV.......D.......Y.MPEAYD......QEKRFSVA..RY.
Retrocopy EFLFPGGFQLSAAEERDMRRKKEVYGLVQDRDKNNDGAGDDYYYRMPEAYDAAANIDQEKRFSVARRRYE

Parental  DPEAKD--KMNPFAEQEAWEEHQIGKSKLQFGSKNRKRSSDDYQYVFEDGIDFVKSSVIEGTQDEDSDDE
          .PEA.D......F.EQEAWEE.QI.KS.LQ.GS..R.R..D.Y...F.DG..FV.SSV..GT...D....
Retrocopy EPEARDGKTAKAFTEQEAWEEQQIRKSMLQLGSTDRGRRGDEYELLFDDGVEFVRSSVMAGTVPDDA-EA

Parental  GADEKDMLKRELQDERKTLPIYKFRDELLKAVEEFQVIVIVGETGSGKTTQIPQYLHEAGYTAKG--KVA
          ..D.K..L..E....RKTLP.YK..D.LLKA..E.QV..IVGETGSGKTTQIPQYLHEAGYTAKG..KVA
Retrocopy AMDAKATLQDE----RKTLPVYKLKDDLLKAIDEYQVLIIVGETGSGKTTQIPQYLHEAGYTAKGKKKVA

Parental  CTQPRRVAAMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTLIKYMTDGMLLREFLGEPDLASYSVVMV
          CTQPRRVAAMSVAARV..EMGVKLGHEVGYS.RFEDCTS.KT.IKYMTDGMLLREFLGEPDL.SYSVV..
Retrocopy CTQPRRVAAMSVAARVAEEMGVKLGHEVGYSVRFEDCTSDKTVIKYMTDGMLLREFLGEPDLGSYSVVVI

Parental  DEAHERTLSTDILFGLVKDISRFRPDLKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTKAPEA
          DEAHERTLSTDILFGLVKDI.RFRPDLKLLISSATL.AEKFSD.FDSAPIF.IPGRR..V.VHYTKAPEA
Retrocopy DEAHERTLSTDILFGLVKDIARFRPDLKLLISSATLNAEKFSDFFDSAPIFRIPGRRFDVAVHYTKAPEA

Parental  DYIDAAIVTVLQIHVTQP--PGDILVFLTGQEEIETIDEILKHRTRGLGTKIAELIICPIYANLPTELQA
          DYIDAAIVTVLQ.HVT.P...GDIL.FLTGQEEIET..EIL..R.R.LG.K.AEL.ICPIYANLPTELQA
Retrocopy DYIDAAIVTVLQLHVTEPAASGDILLFLTGQEEIETVEEILRQRLRVLGGKVAELVICPIYANLPTELQA

Parental  KIFEPTPEGARKVVLATNIAETSLTIDGIKYVVDPGFCKIKSYNPRTGMESLLINPISKASANQRAGRSG
          KIFEP.PEGARKVVLATNIAETSLTIDGIKYVVDPGFCK.KSYNPRTGMESLL..P.SKASA.QRAGRSG
Retrocopy KIFEPAPEGARKVVLATNIAETSLTIDGIKYVVDPGFCKVKSYNPRTGMESLLVAPVSKASAEQRAGRSG

Parental  RTGPGKCFRLYTSYNYMHDLEDNTVPEIQRTNLANVVLTLKSLGIHDLVNFDFMDPPPSEALLKALEQLF
          RTGPGKCFRLYT.YN...DL...TVPEIQR.NLANVVL.LK.LGI.DLV.FDFMDPP..E.LLKALE.LF
Retrocopy RTGPGKCFRLYTEYNFLNDLDADTVPEIQRSNLANVVLALKTLGINDLVGFDFMDPPAAESLLKALEELF

Parental  ALSALNSRGELTKTGRRMAEFPLDPMLSKMIVASEKYKCSDEVISIASMLSVGNSIFYRPKDKQVHADNA
          AL.ALNSRGELTKTGRRMAEFPLDPMLSK.IVASEKY.CS.EVI.IA.MLS.GN..FYRPKDKQVHAD.A
Retrocopy ALGALNSRGELTKTGRRMAEFPLDPMLSKAIVASEKYGCSEEVITIAAMLSAGNAVFYRPKDKQVHADAA

Parental  RLNFH-TGNVGDHIALLNVYNSWRETDYSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEVSTNASD
          R..FH..GNVGDH.ALLNVYN.WRE..YS.QWC.E...Q.R.M.RARD.R.QL..LLERVEI.....A.D
Retrocopy RRAFHAAGNVGDHVALLNVYNAWRESGYSAQWCRESFVQHRTMRRARDVRGQLVALLERVEIAPCSAAGD

Parental  LDAIKKAITSGFFHHSARLQKNGSYRTVKNPQTV
          L.A..KAIT.G.F.H.ARLQ..GSYR.VK..QTV
Retrocopy LGAVRKAITAGYFRHAARLQRDGSYRAVKSRQTV

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_14 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 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14 ,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,