RetrogeneDB ID: retro_lper_20

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 1:67815..69414(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR01G00120
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR01G38640
• Aliases: None
• Description: None

Sequence

>retro_lper_20
ATGTCCATGGCTCATCGGCGCTCACCGGCGGGGGCAATTCTGGTCCTAATAATGCTGGTGGCGGCGGAGGCAGCGGGGAC
GAAGAAGAGCCCGATCAAGAATGTGGTGGTGCTGGCGCTGGAGAACCGGTCGTTCGACCACATGCTGGGGTGGATGCGCA
CCATGCTGGGCCTCCCCATCGACGGCCTCACCGGCGCAGAATGCAATCCAGCGGGGATTGGGTGGCGGTGCGTGTCCCCG
GACGCGGAGCTGGTGGTCCCCGACGACCCCGCCCACGCCTTCGAGGACGTCCTCGAGCAGCTGCTCGGATTCCGCCCCAA
CTCTTCCTTGGACGCTTACGCCTCCGACATGTCGGGCTTCGTCCGCAGCGCCGACGGCGTGAGCGCGGTGCTGAGCGAGG
CCGTGATGCGGGGCTTCAGGCCGTCGCGGCTTCCGGCGTTCTCGGCGCTGGCGTCGTCGTTCGCGGTGTTCGACCGGTGG
TTCTCGTCCATCCCGGGCCCCACGCAGCCCAACCGGCTGTTCCTCTACTCCGCCACCTCCCACGGCGCCGTCGCCCACGA
CAAGTGGAACCTCCTCCGCGGCTACCCGCAGCGCACCATCTTCGACTCCCTCGCCGCCGCCGGCCTCGACTACAGGGTCT
ACTTCAAGACCATCCCCACCACCCTCTTCTACCGCCGCCTCCGCACCATCGCCAATTTCGACAGGTTCCGCCGCTACGAC
TCCTCCTTCCTCGACGACGCCCGCCGCGGCCTCCTCCCGGCGCTGACCGTCATCGAGCCACGCTACTTCCATCTCACGGG
GACGCCCGCCGACGACGACCACCCGGCGCACGACGTCGGCAACGGCCAACGCCTAGTGAAGGAGGTGTACGAGGCGCTGC
GCGGTGGGCCGCAGTGGAATCAGACGCTGCTCATCATCACCTACGACGAGCACGGCGGCTTCTACGACCACGTGCCGCCG
CCCAACGTGGGCGTGCCCAACCCCGACGGCATTCGCGGGCCATTCCCTTTCTTCTTCAACTTCGACCGGCTCGGCGTCAG
GGTGCCCACCATCATGGTCTCGCCATGGATCAGGAAGCAAACCGTCGTCGGCCGCCCGCCGCATGGGAGTGGCGCCGAGT
ACGAGCACTCCTCCATTCCGGCCACCATCAAGGCGATTTTCAACCTCAGCTCCGACTTCCTCACAAGGAGAGACGCCTGG
GCGGGCACATTCCACCACATCTTCGACGAGCTGGACGAGCCCAGGGCGGACTGCCCGGAGAAATTGCCGGACGTGCCGCC
GCCTCCTTCCGGAGGTGCCTCCTCGGCCAAGGGAAACGGCGGCTTCCTGTCCGATTTCCAGCGGGAGCTCGTCCAGCTGG
CCGCATTCCTCAACGGCGACTACATGCTCACCACCAGCGCCGCAGTCTCATCAAAGCAAGATCGGAGGATGACGGTGAAG
GAGGCGGACGCGTACGTGAAGCGAGCGGTGAAGAGTTTTCTGGAGGCCAGCAAGCGTGCCAAACGCTTAGGCGCCAACGA
CTCCGCCATTGTAACCATGAGGCCTTCCTTGACCACTGCCTCTGCTTCTGCCTCAACTTCAACAGACTGCTGCTCTTAA

Alignment

ORF - retro_lper_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.97 %
• Parental protein coverage: 76.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGFVQQARSLGGDMTGAVMNGFSPDSVAVYRDLVAEFAVFDRWFASVPSSTQPNRLFVHSGTSGGATSN
          M.GFV..A.........AVM.GF.P........L...FAVFDRWF.S.P..TQPNRLF..S.TS.GA...
Retrocopy MSGFVRSADGVSAVLSEAVMRGFRPSRLPAFSALASSFAVFDRWFSSIPGPTQPNRLFLYSATSHGAVAH

Parental  NPALLAKGYPQQTIFDNVHDAGLSFGVYYQDVPAVLFYRNLRKLKYLTKFHPFHNAFRDHAARGDLPNYA
          ....L..GYPQ.TIFD....AGL...VY....P..LFYR.LR.......F......F.D.A.RG.LP...
Retrocopy DKWNLLRGYPQRTIFDSLAAAGLDYRVYFKTIPTTLFYRRLRTIANFDRFRRYDSSFLDDARRGLLPALT

Parental  VVEQHYMDSRLHPANDDHPSHDVFQGQMLVKEVYETLRASPQWNQTLMVVTYDEHGGFFDHVPTPVKGVP
          V.E..Y......PA.DDHP.HDV..GQ.LVKEVYE.LR..PQWNQTL...TYDEHGGF.DHVP.P..GVP
Retrocopy VIEPRYFHLTGTPADDDHPAHDVGNGQRLVKEVYEALRGGPQWNQTLLIITYDEHGGFYDHVPPPNVGVP

Parental  SPDGIVGPPPYNFTFDRLGVRVPTIVISPWINKGTVV-HGPNGSPTPTSEYEHSSIPATVKKIFNLPQDF
          .PDGI.GP.P..F.FDRLGVRVPTI..SPWI.K.TVV...P.GS.....EYEHSSIPAT.K.IFNL..DF
Retrocopy NPDGIRGPFPFFFNFDRLGVRVPTIMVSPWIRKQTVVGRPPHGSG---AEYEHSSIPATIKAIFNLSSDF

Parental  LTKRDAWAGTFETVVQTRTEPRTDCPEQL----PMPTRIRMTEANEEAKLSEFQQELVQLASVLNGDHQL
          LT.RDAWAGTF........EPR.DCPE.L....P.P.............LS.FQ.ELVQLA..LNGD..L
Retrocopy LTRRDAWAGTFHHIFDELDEPRADCPEKLPDVPPPPSGGASSAKGNGGFLSDFQRELVQLAAFLNGDYML

Parental  NSLQDMIRDRMNVREGIDYMHTAVKRFFEAGMSA----KRMGVDDEQIVKMRPSLTTRTSPA
          .............R.........VKR.......A....KR.G..D..IV.MRPSLTT....A
Retrocopy TT-SAAVSSKQDRRMTVKEADAYVKRAVKSFLEASKRAKRLGANDSAIVTMRPSLTTASASA

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_20 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA000088	1 retrocopy	retro_oind_49,
Brachypodium distachyon	BRADI2G61140	1 retrocopy	retro_bdis_16,
Leersia perrieri	LPERR01G38640	1 retrocopy	retro_lper_20 ,
Oryza barthii	OBART01G44250	2 retrocopies	retro_obar_19, retro_obar_5,
Oryza glumaepatula	OGLUM01G48550	1 retrocopy	retro_oglu_24,
Oryza nivara	ONIVA01G50380	1 retrocopy	retro_oniv_1,
Oryza glaberrima	ORGLA01G0381200	1 retrocopy	retro_ogla_34,
Oryza rufipogon	ORUFI01G47680	2 retrocopies	retro_oruf_3, retro_oruf_32,