RetrogeneDB ID: retro_lper_23

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 6:309652..310426(-)
• Located in intron of: LPERR06G00530

Retrocopy information

• Ensembl ID: LPERR06G00540
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR10G14940
• Aliases: None
• Description: None

Sequence

>retro_lper_23
ATGATGAGCTCCAAGCTTGCAAGCTCGCCGGCGACAATGGAGAAGACGACGGCGACTCCGACTCCGGTGGAGGCGGTGCT
GTTCGACATCGACGGCACGATGTGCGTGTCGGACCCATTCCATCACAGGGCCTTCTCAGAGCTTCTCCAGAAGCTGGGCT
ACAACTCCGGCGTCCCAATCTCGCCGGAGTTCGGGATGGCCCACATGGCCGGCCGGAGCAACGACCAGATCGGCCGCTTC
CTCTTCCCGGAGTGGGGCCAGGACCAGCTCGATGCCTTCTTTGCCGAAAAGGAGGCCCTTTTCGCCCGCTATGCCGGCGA
GGGCCTCCGGGAGATCGCCGGAGTTACCGACTACTGCCGGTGGGCCGCTGGCCATGGCCTCAAGCGGGCCGCCGTCACCA
ACGCGCCGCGGGCCAACGCCGAGCTCATGATCTCCATCCTTGGCCTGTCTGATTTCTTCCAGGTCATCGTCTCCGCCGCC
GATGACTGTGATCTCCCCAAGCCTTCGCCGGAGCCTTACCTCCGGGCGCTCAGCCTGCTCGGAGTTTCTGCCGATCAGGC
CATCGTCTTCGAGGACTCGGTCATCGGGGTGCAGGCCGGCGTCGCAGCCGGGATGCCGGTGATCGCCGTCGCGGAGGAGA
GCCGGGAGGCCAAGGTCGTCGCCGCCGGAGCGTCGCTGGTCATCAGGGACTACAAGGATGACAAGCTCTGGGCAGCTTTA
GACAAGCTCAACACCGCAGCAGCAGCTCAAGTAGATGGAGAACTTGGAGCATAG

Alignment

ORF - retro_lper_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.53 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLEAILFDIDGTLCDSDPIHFCAFRDLLQQVGFNNGVPITEEFYSANISGGHNDDLARALFPDLDHDKAM
          P.EA.LFDIDGT.C.SDP.H..AF..LLQ..G.N.GVPI..EF..A...G..ND...R.LFP....D...
Retrocopy PVEAVLFDIDGTMCVSDPFHHRAFSELLQKLGYNSGVPISPEFGMAHMAGRSNDQIGRFLFPEWGQDQLD

Parental  KFMDDKEAFFRKLAPEQLKAVDGLHDLCRWIDAHKLKRAAVTNAPRSNAELMLSLLGLTDFFPVLV-IGS
          .F...KEA.F...A.E.L....G..D.CRW...H.LKRAAVTNAPR.NAELM.S.LGL.DFF.V.V....
Retrocopy AFFAEKEALFARYAGEGLREIAGVTDYCRWAAGHGLKRAAVTNAPRANAELMISILGLSDFFQVIVSAAD

Parental  ECDRAKPFPDPYLKALELIDASPDHTFIFEDSASGIRAGVAANVPVVGLTTRNPEKVLNDAGASLLIKDF
          .CD..KP.P.PYL.AL.L...S.D....FEDS..G..AGVAA..PV........E.....AGASL.I.D.
Retrocopy DCDLPKPSPEPYLRALSLLGVSADQAIVFEDSVIGVQAGVAAGMPVIAVAEESREAKVVAAGASLVIRDY

Parental  QDPKLLAILDELKPAVAVE
          .D.KL.A.LD.L..A.A..
Retrocopy KDDKLWAALDKLNTAAAAQ

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_23 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	LPERR10G14940	1 retrocopy	retro_lper_23 ,
Oryza brachyantha	OB10G26200	1 retrocopy	retro_obra_11,