RetrogeneDB ID: retro_lper_16

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 4:22551785..22553063(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR04G25270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR02G06920
• Aliases: None
• Description: None

Sequence

>retro_lper_16
ATGTCCGCAAGCAGCGAGAGAAAATCCCCGAATTGGCCGATCGCGACGGCGGCGGCGGCGGCCGGAGATGGGCAGGCGGC
CGTGAAGGGGAGGGGCAGCGGCGACGGCGAGGAGATCCGTCTGTACTATGAGCAATACGTCCAGGATCTGCACCTCCATC
TCCGCCAAAAAGAGGACGACATCAGCCGCCTCGAGGCCGAGCGCAATGGCCTCAGCTCGCGAGTCAGTGTGATGAGCAAA
GAGGTGCGGTTGCTTCAAGCGAAGGAATCGTATCTCGGTGAGGTTGTCAAGGTTATGGGGAAGTCCAAGGTTCTAGTGGA
TGCGTATCAAAAAGGGAAATTCGTCGTCGATGTTGACAGAAGCATCGATGTCACGGATCTCACGCCTTCGACGAGAGTTG
CTCTTCGAAACGACGGCAGCTACACGCTTCATCTTGTCCTGGCCAGCAAGGTTAATCCGTTCGTTAATTTTATGAAGGTT
GAGAAGGTTCCTAATTCTACTTATGATATGATTGGAGGACTTGATCAGCAGATTAACGAGATCAAAGAGGTGATTGAGCT
TCCAATTAAGCATCCTGAGCTGTTTGAAAGTCTTGGGATTACCCAGCCAAAGGGGGTTCTTCTTTATGGACCTCCTGGTA
CTGGAAAAACGCTGTTGGCTCGAGCAGTTGCTCATCACACTGACTGTACCTTCATTAGAGTGTCAGGTTCTGAGTTGGTT
CAGAAGTATATTGGAGAGGGTTCAAGAATGGTTCGTGAACTCTTTGTGATGGCTAGAGAGCATGCACCATCCATAATCTT
TATGGATGAAATAGACTCCATTGGATCTGCTCGAATGGAGTCTGGACCTCACGGTGGTGATAATGAGGTTCAACGCACTA
TGATCGAGCTTCTCAACCAACTTGATGGCTTTGAAGCGAAAAACAATATTAAGGTTATTATGGCCACAAACAGGATGGAT
GTATTGGATCAAGCTCTCTTGAGGCCCGGACGAATCGATAGGAAGATTGAATTCCCAAATCCGAATGAAGATTCCCGTTT
TGACATCTTGAAGATTCATTCGAGAAGGATGAACTTGATGGGTGGAGTTGATCTGAAGAAAATTGCGGCGAAGATGAATG
GAGCAAATGGTGCAGAGCTGAAGGCGGTATGCACTGAAGCAGGAATGTTTTCCATTCGAGAAAGAAGGGTTCATGTCACA
CAGGAGGACTTCGAAATGGCCGTGCCAAAAGTGATGAAGAAGTATACCGAACATAACATGTCCATGTTGAAGTTCTAG

Alignment

ORF - retro_lper_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 96.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AATGDEAAAAKGRGGGGGGGEGLRQYYLQHIHDLQLQIRQKTHNLNRLEAQRNDLNSRVRMLREELQLLQ
          AA.GD..AA.KGRG.G.G..E..R.YY.Q...DL.L..RQK.....RLEA.RN.L.SRV.....E..LLQ
Retrocopy AAAGDGQAAVKGRGSGDG--EEIRLYYEQYVQDLHLHLRQKEDDISRLEAERNGLSSRVSVMSKEVRLLQ

Parental  EPGSYVGEVVKVMGKSKVLVKVHPEGKYVVDIDKSIDITKITPSTRVALRND-SYMLHLILPSKVDPLVN
          ...SY.GEVVKVMGKSKVLV.....GK.VVD.D.SID.T..TPSTRVALRND.SY.LHL.L.SKV.P.VN
Retrocopy AKESYLGEVVKVMGKSKVLVDAYQKGKFVVDVDRSIDVTDLTPSTRVALRNDGSYTLHLVLASKVNPFVN

Parental  LMKVEKVPDSTYDMIGGLDQQIKEIKEVIELPIKHPELFESLGIAQPKGVLLYGPPGTGKTLLARAVAHH
          .MKVEKVP.STYDMIGGLDQQI.EIKEVIELPIKHPELFESLGI.QPKGVLLYGPPGTGKTLLARAVAHH
Retrocopy FMKVEKVPNSTYDMIGGLDQQINEIKEVIELPIKHPELFESLGITQPKGVLLYGPPGTGKTLLARAVAHH

Parental  TDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSARMESGTGNGDSEVQRTMLE
          TDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSARMESG...GD.EVQRTM.E
Retrocopy TDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSARMESGPHGGDNEVQRTMIE

Parental  LLNQLDGFEASNKIKVLMATNRIDILDQALLRPGRIDRKIEFPNPNEDSRFDILKIHSRKMNLMRGIDLK
          LLNQLDGFEA.N.IKV.MATNR.D.LDQALLRPGRIDRKIEFPNPNEDSRFDILKIHSR.MNLM.G.DLK
Retrocopy LLNQLDGFEAKNNIKVIMATNRMDVLDQALLRPGRIDRKIEFPNPNEDSRFDILKIHSRRMNLMGGVDLK

Parental  KIAEKMNGASGAELKAVCTEAGMFALRERRVHVTQEDFEMAVAKVMKKDTEKNMSLRK
          KIA.KMNGA.GAELKAVCTEAGMF..RERRVHVTQEDFEMAV.KVMKK.TE.NMS..K
Retrocopy KIAAKMNGANGAELKAVCTEAGMFSIRERRVHVTQEDFEMAVPKVMKKYTEHNMSMLK

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_16 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR02G06920	1 retrocopy	retro_lper_16 ,
Leersia perrieri	LPERR02G11870	1 retrocopy	retro_lper_5,