RetrogeneDB ID: retro_lper_10

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 1:32730974..32732324(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR01G40060
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR05G00860
• Aliases: None
• Description: None

Sequence

>retro_lper_10
ATGGGGCAGGGCCTGAGCTGCAGCCGCGACACCGTCGAGCACGACTTCTTCCTCGCCGCCAAGGCCGGCGACGTCCACGC
CCTGCGCGCCCACCTCGCCGCCGACCCCTCCCTCGCCCGCCGCGCCACCGTCTACGCCCGCTCCACCGCCCTCCACATCG
CCGCCGCCAATGGCCGCGTCGAGGCGGTATCCATGCTGCTCGACCGCGGCGACGTGCACCCCGACGCGCTCAACCGCAAG
AAGCATACGCCGCTGATGCTGGCGTCGAAGCGCGGGAACACGGAGTGCGTTGTCAGGCTCCTCGACGCCGGCGCCAACGT
GCTGACGTTCGAGTCGCGTCGAGCCAGGACGTGCCTCCACCACGCCGCCTACCACGGCCACGCCGACTGCCTCCACGCCA
TCCTCGCCGCCGCCGACGGACACGGCGTGGCGGCGTCGTGGGGATTCGCGCGGTTCGTGAACGTTCGGGACGAGCAGGGC
GCGACGCCGCTGCACCTGGCGGCGAGGCGTGGGCGATCGGCGTGCGTGCGGCTGCTGCTGGGAAGGGGCGCAATCGTGTC
GGCGTCCACGTCCGTGTACGGCTTCCCGGGCAGCACGGCGCTGCACCTGGCGGCGCGCGGCGGCGACATGGAGTGCGCGC
GCGAGCTGCTGGCGTGGGGCGCCGACAGGATGCAGAGGGATTCGGCGGGGAGGATCGCGTACGTGGTGGCGCTCCGGCGT
GGGCACCGCGCGTGCGCCGCGCTGCTGAACCCGGCGGCGGCGGAGCCCATGGTGTGGCCGTCGCCGCTCAAGTTCATCGC
GGAGCTCGACGCCGACGCCAAGGCGCTGCTGGAGAAGGCGCTCGTGGACGCCAACAGGGAGAGGGAGAAGGCCATCCTAC
GAAACCTCAACCACAAGCAGGTCATGCCGTCCAACACTGATGTTGTTGTTGATGCCGACGAGGACGACCAAGAGGTGTGC
AACATCTGCTTCGAGCAGGCGTGCAGCATGGAGGTGAAGGAGTGCGGGCATGAGATGTGCGCGGCCTGCACTCTGGCGCT
CTGCTGCCACTGCAAGCCCAACCCCAAGACTCTGCTGCTCCAGCCGCCGGCCTGCCCGTTCTGCCGCACCACCATCTCAC
GCCTCGTCGCCAAGGTGTCCGACACCGACAGACGACGACTGAGCCGCCGGCGGTCGAGGACATCTCGCGACGGCGGCGGC
AGCAGCAGCTTCAAGGGGCTCTCGTCGGCCATGGGGTCGTTTTCCAGGATAGGGCGAGGCTCCGGGAGATTGGTGGTTGA
TGACGGAGCCGAGCTCACGGACAAGCCAACTTCTGATCACGACCTCTCTTCTGTCGTCGGTGTCCTCTGA

Alignment

ORF - retro_lper_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.44 %
• Parental protein coverage: 94. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGHGVSCARTGDEHDFFRAAQVGDLDALAALLAADQSLARRATLYDRLSVLHIAAANGRIEVLSMFLDRG
          MG.G.SC.R...EHDFF.AA..GD..AL.A.LAAD.SLARRAT.Y.R...LHIAAANGR.E..SM.LDRG
Retrocopy MGQGLSCSRDTVEHDFFLAAKAGDVHALRAHLAADPSLARRATVYARSTALHIAAANGRVEAVSMLLDRG

Parental  -APPDAVNRHKQTPLMLAAMHGKIDCVLKLLQAGANILMFDSVHARTCLHHAAYYGHVDCLQAILSAAQT
          ...PDA.NR.K.TPLMLA...G...CV..LL.AGAN.L.F.S..ARTCLHHAAY.GH.DCL.AIL.AA..
Retrocopy DVHPDALNRKKHTPLMLASKRGNTECVVRLLDAGANVLTFESRRARTCLHHAAYHGHADCLHAILAAADG

Parental  TPVADSWGFARFVNVRDDHGATPLHLAARQGRPGCVQMLLENGAIVSALTGSYGFPGSTSLHLAARSGNL
          ..VA.SWGFARFVNVRD..GATPLHLAAR.GR..CV..LL..GAIVSA.T..YGFPGST.LHLAAR.G..
Retrocopy HGVAASWGFARFVNVRDEQGATPLHLAARRGRSACVRLLLGRGAIVSASTSVYGFPGSTALHLAARGGDM

Parental  DCIRKLLAWGADRLQRDSAGRIPYSVALKRNHGACAALLNPSSAEPMVWPSPLKFISELDPEAKALLEAA
          .C.R.LLAWGADR.QRDSAGRI.Y.VAL.R.H.ACAALLNP..AEPMVWPSPLKFI.ELD..AKALLE.A
Retrocopy ECARELLAWGADRMQRDSAGRIAYVVALRRGHRACAALLNPAAAEPMVWPSPLKFIAELDADAKALLEKA

Parental  LMEANREREKKILNGTKYSLPSPPPYDDSADEDACSEVSDAELCCICFDQACTIEVQDCGHQMCAPCTLA
          L..ANREREK.IL.........P...D...D.D......D.E.C.ICF.QAC..EV..CGH.MCA.CTLA
Retrocopy LVDANREREKAILRNLNHKQVMPSNTDVVVDADE----DDQEVCNICFEQACSMEVKECGHEMCAACTLA

Parental  LCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKPASPQLTRRRSRRSHNLS--EGSSSFKG
          LCCH.KPNP.TL....PACPFCR..ISRLV........D.D.........R.SR.....S...G.SS..G
Retrocopy LCCHCKPNPKTLLLQPPACPFCRTTISRLVA----KVSDTDRRRLSRRRSRTSRDGGGSSSFKGLSSAMG

Parental  LSSAMG
          ..S..G
Retrocopy SFSRIG

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_10 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA018946	1 retrocopy	retro_oind_45,
Leersia perrieri	LPERR05G00860	1 retrocopy	retro_lper_10 ,
Oryza barthii	OBART05G00890	1 retrocopy	retro_obar_26,
Oryza glumaepatula	OGLUM05G00910	1 retrocopy	retro_oglu_21,
Oryza meridionalis	OMERI05G00950	1 retrocopy	retro_omer_12,
Oryza nivara	ONIVA05G00830	1 retrocopy	retro_oniv_6,
Oryza punctata	OPUNC05G00800	1 retrocopy	retro_opun_25,
Oryza glaberrima	ORGLA05G0009300	1 retrocopy	retro_ogla_12,
Oryza rufipogon	ORUFI05G00870	1 retrocopy	retro_oruf_36,
Oryza sativa japonica	OS05G0112000	1 retrocopy	retro_osat_41,