RetrogeneDB ID: retro_lper_3

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 3:29401239..29402340(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR03G35520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR01G34060
• Aliases: None
• Description: None

Sequence

>retro_lper_3
ATGGTGCAGCAGCAGCAGCATGAGGATATGGATAAGTTGGTGTTCGACGCGGCGGTGCTGAGCGGCGAGAGGGAGATCCC
GTCGCAGTTCATCTGGCCGGCGGAGGAGAGCCCCGGGTCGGTGGAGGCGGAGGAGCTGGACGTGCCGCTCATCGACGTGG
GCGCCGGCGTCGACAGCGACGAGGTTGTCCGCCTCGTCGGCGAGGCGTGCGAGAGGCACGGCTTCTTCCTGGTGGTGAAC
CACGGCATCCCGTGGTCACTCCTGGAGGAAGCACACCGGTGCATGGACGCCTTCTTCACGCTGCCTCTGGCCTCCAAGCA
GCGCGCCCAGCGCCGGCCCGGCGAGAGCTGCGGCTACGCGAGCAGCTTCACCGGCCGCTTCGCGTCCAAGCTGCCGTGGA
AGGAGACGCTCTCCTTCCGCTACTCCTCCGGCGGCGGCGACGGCGTGGCGGATTATTTGGCTGGGAAGCTTGGGGAGGAG
CACGGCCGGCATCTGGGCGATGTGTACGAGCGCTACTGCGGCGAGATGAGCCGTCTGTCGCTGTATCTGATGGAGGTGCT
GGGCGAGAGCCTGGGGGTGGGTCGCCGCCACTTCCGGCGCGTGTTCGAGAGGAACGACTCCATCATGCGGCTCAACTACT
ACCCGTCGTGCCAGCGGCCGCGTGAGACGCTGGGCACGGGCCCGCACTGCGACCCCACGTCGCTGACCATCCTCCACCAG
GACGACGTGGGCGGCCTCGAGGTTTGGGCGGAGGGGACGTGGCGGAGCATCCGCCCGCGTCCCGGCGCGCTGGTCGTCAA
CGTCGGCGACACCTTCATGGCGCTCTCCAACGGCAGGTACAGGAGCTGCCTCCACCGTGCCGTGGTCAACAGCAGGTCGC
CGCGGCGGTCGCTGGCCTTCTTCCTCTGCCCGGAGATGGACATGGTGGTCACGCCGCCGAGTCAGCTCGTCGACGACCGC
TACCCCAGGGCGTACCCCGACTTCACGTGGCGGTCGCTGCTCGACTTCACGCAGCGACACTACCGGTCCGACATGCGCAC
GCTCCAGGCCTTCTCCCACTGGCTCAACCTGCAGCAGCACACCACCACTGCTGCTACCTAG

Alignment

ORF - retro_lper_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.25 %
• Parental protein coverage: 88.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRRDPKIPEPFVWPNADARPASARELDMPVVDVAVLRNGDADGLRRAVAQVASACATHGFFQVSGHGVDA
          L.....IP..F.WP.A...P.S.......V....V....D.D...R.V.....AC..HGFF.V..HG...
Retrocopy LSGEREIPSQFIWP-AEESPGSVEAEELDVPLIDVGAGVDSDEVVRLVGE---ACERHGFFLVVNHGIPW

Parental  GLARAALDGASDFFRLPLAEKRRARRVPGTVSGYTSAHADRFASKLPWKETLSFGFHDHNNTPVVADYFS
          .L...A......FF.LPLA.K.RA.R.PG...GY.S....RFASKLPWKETLSF..........VADY..
Retrocopy SLLEEAHRCMDAFFTLPLASKQRAQRRPGESCGYASSFTGRFASKLPWKETLSFRYSSGGGDG-VADYLA

Parental  STLGPDFA-PMGRVYQKYCEEMKELSLTIMELLEVSLGVERGYYREFFADSSSIMRCNYYPPCPEPERTL
          ..LG.......G.VY..YC.EM..LSL..ME.L..SLGV.R...R..F....SIMR.NYYP.C..P..TL
Retrocopy GKLGEEHGRHLGDVYERYCGEMSRLSLYLMEVLGESLGVGRRHFRRVFERNDSIMRLNYYPSCQRPRETL

Parental  GTGPHCDPTALTILLQDDVGGLEVLVDGEWRPVNPVPGAMVINIGDTFMALSNGRYKSCLHRAVVNQRKE
          GTGPHCDPT.LTIL.QDDVGGLEV...G.WR...P.PGA.V.N.GDTFMALSNGRY.SCLHRAVVN.R..
Retrocopy GTGPHCDPTSLTILHQDDVGGLEVWAEGTWRSIRPRPGALVVNVGDTFMALSNGRYRSCLHRAVVNSRSP

Parental  RRSLAFFLCPREDRVVRPPPSAAT---PRNYPDFTWADLMRFTQRHYRADTRTLDAFTRWL
          RRSLAFFLCP..D.VV.PP........PR.YPDFTW..L..FTQRHYR.D.RTL.AF..WL
Retrocopy RRSLAFFLCPEMDMVVTPPSQLVDDRYPRAYPDFTWRSLLDFTQRHYRSDMRTLQAFSHWL

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_3 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR01G34060	1 retrocopy	retro_lper_3 ,
Oryza barthii	OBART01G39570	1 retrocopy	retro_obar_12,
Oryza meridionalis	OMERI01G36440	1 retrocopy	retro_omer_11,
Oryza glaberrima	ORGLA01G0334700	1 retrocopy	retro_ogla_32,
Oryza sativa japonica	OS01G0883800	1 retrocopy	retro_osat_2,
Setaria italica	Si001573m.g	1 retrocopy	retro_sita_29,