RetrogeneDB ID: retro_lper_5

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 9:14883755..14885132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR09G15440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR02G11870
• Aliases: None
• Description: None

Sequence

>retro_lper_5
ATGGCCACCGCCACGACGCTTCAACCACCTCTCCCGTGTCCGGCCACCGCCGCCGCCGCCCACGACATCTTCGCCGGCGA
CGAGCAGCAGCAGCAGAAGAAGAAGCCCTTTTACCTTGAGGAGGAAGAGGACGACTTGGTCGACGACGATCTCCTCTACC
TCGACGACGACCTACGTCAGCAAGTGATGTCAGCGGAGCGTCACCTCTGTTCCCTCGACGAGAAGTACGACCACGCGCTG
CAGGAGATTCACAACCTGACGAAAGAATTCGTCGCCGACGAGGCGGAGATGCGGCTGATGCTGCCGCCGTTCGCCCCCCT
CGTCGCCGCCGAGCTCGACGAGATTCTCTCCGACGACCTCGCCGTCGTCACCATCCCCCACCACCACGGCGGCGGCGGCT
GCGGCGAGAGATTCGTCGTGCCCGTCCTCCCCTCGCTCGACCGCGCCCTCCTCACGCCGCCGGCGAGCGTCGCGCTCCAC
GGCGGCAAGTCGATGGCGCTCGTCGCCGTTCTCCCTCCCGACGCCGCCGCGACGGCGGCGGCGGCGTTCGAGGTGTCCGG
CGCCGACATGCCGGAGCTGACGTACGATGACATTGGGGGAATGGAGGAGCAGAAGAGGGAGGTGAGGGAAGCCATCGAGC
TGCCGTTGACGCAGCCGGAGCTCTTCGCCGCCGCGGGGATCGACCCGCCACGTGGCGTGCTCCTGTACGGCCCGCCGGGG
ACGGGGAAGACGATGCTCGTCAAGGCCGTCGCGCGCGCCACGGCGAACGCGGCGGCGTTCTTCCGCCTCACCGGCGCCGA
CCTCGTCGCCGGCGGAGGCGCGAGGATGGTGCGTGACGTGTTCCGCCTCGCGAGGGAGAAATCCCCGTCCATCGTGTTCA
TCGACGAGGCCGACGCCGTCGCCGCGGCGCGTCGCGACGGCGGCGACGGCGACGGCGGCGCGGCGAGGCATGTCAACCGC
GTTCTGATCGAGCTGCTCACCCAGATGGACGGCTTCGACGGCGACGGCGACGCCGGCGTGAGGGTGATCATGGCGACGAA
CAACGCCGGCGACATGGACCCGGCGCTGCTGCGGCCGGGGAGGATAGACAGGAAGGTGGAGTTCACGGCGCCGAGGAGCA
CGGAGGAGAGGAGGATGGTGCTCGACGCGTGCGCCAAGGGGATGAGCCTCGACGGTGGCGTCGACCTTGATGACGTGGCA
AAGCGGCGCGACGGGATGAGCGCCGCGGAGATCGCCGCCGTTTGCCGCGAGGCCGGCATGCGGGCCATCCGCGACGGGCG
GTGCACGGTGACCGGAGACGACTTTGACCAGGGTTATCATGCCGTCGTCGGCAAGATGCCCCGCGACGTCGCCGCCGAGT
TTCAATTCTACAACTGA

Alignment

ORF - retro_lper_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.8 %
• Parental protein coverage: 73.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSTTGSNYYVRILSTINRELLKPSASVALHR-HSNALVDVLPPEADSSISL---LGSSEKPNVTYTDIGG
          G...G....V..L....R.LL.P.ASVALH...S.ALV.VLPP.A...............P..TY.DIGG
Retrocopy GGGCGERFVVPVLPSLDRALLTPPASVALHGGKSMALVAVLPPDAAATAAAAFEVSGADMPELTYDDIGG

Parental  CDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHT--TAAFIRVVGSEFVQ
          ...QK.E.REA.ELPLT..EL....GIDPPRGVLLYGPPGTGKTML.KAVA..T...AAF.R..G...V.
Retrocopy MEEQKREVREAIELPLTQPELFAAAGIDPPRGVLLYGPPGTGKTMLVKAVARATANAAAFFRLTGADLV-

Parental  KYLGEGPRMVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTG---ADREVQRILMELLNQMDGF--DQT
          ...G.G.RMVRDVFRLA.E..P.I.FIDE.DA.A.AR.D...G...A.R.V.R.L.ELL.QMDGF..D..
Retrocopy --AGGGARMVRDVFRLAREKSPSIVFIDEADAVAAARRDGGDGDGGAARHVNRVLIELLTQMDGFDGDGD

Parental  VNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP-DRRQKRLVFQVCTAKMNLSDEVDLEDYVSRPDKIS
          ..V.VIMATN.A...DPALLRPGR.DRK.EF..P......R.V...C...M.L...VDL.D...R.D..S
Retrocopy AGVRVIMATNNAGDMDPALLRPGRIDRKVEFTAPRSTEERRMVLDACAKGMSLDGGVDLDDVAKRRDGMS

Parental  AADIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPETD
          AA.IAA.C.EAGM.A.R..R......DF..GY...V.K...D
Retrocopy AAEIAAVCREAGMRAIRDGRCTVTGDDFDQGYHAVVGKMPRD

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_5 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008091	1 retrocopy	retro_oind_47,
Aegilops tauschii	F775_28952	1 retrocopy	retro_atau_13,
Leersia perrieri	LPERR02G06920	1 retrocopy	retro_lper_16,
Leersia perrieri	LPERR02G11870	1 retrocopy	retro_lper_5 ,
Oryza barthii	OBART02G14640	1 retrocopy	retro_obar_11,
Oryza punctata	OPUNC02G13140	1 retrocopy	retro_opun_13,
Oryza glaberrima	ORGLA02G0127200	1 retrocopy	retro_ogla_44,
Oryza sativa japonica	OS02G0325100	1 retrocopy	retro_osat_48,