RetrogeneDB ID: retro_oglu_4

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 9:9509124..9510219(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM09G06240
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM05G20150
• Aliases: None
• Description: None

Sequence

>retro_oglu_4
ATGGCGGAGGTGTGCTGTGATTCTGCGGTGGTGGTCGGGGCGGGGGCGGGGGCGGAGGCGGAGGCGAGGGCGAGGGCGCG
CGCCGGGAGGCGGCGGCGGGCGGGAGTTGAGGGGGCAGGGAGGTGGAACGCCACGGCGACGGCTGCGGGTGTGGCGGCGG
AGGAGGCCGCGACGAGGAAGCGGAGGGCGAGTGGTGGTGAGGCCGGGTTGGTGGTGGTGGCGAAGCGGCATGGGGCGGCG
TCGGTCGCCGGGAGGAGGAGGGAGATGGAGGACGCCGTGTCGCTGCGCGAGGCGTTCGCCGCGCCGGCGGACGGGGAGGT
TGCGGCGGCGAGGTGTGACTTCTATGGGGTGTTCGACGGGCACGGCTGCTCGCACGTGGCGGACGCGTGCAGGGAGCGGA
TGCACGAGCTCGTCGCGGAGGAGATGGGCGCCGGGTCACCGGCGGTGGCGGCGGCGGCGGCGGCGCGCGAGCCGGCGTCT
TGGACGGGGGTGATGGAGCGGAGCTTCGCGAGGATGGACGCCGAGGTGATCGCCGGCTGCCGAGCCGAGAGCGGCAGCTG
CCGGTGCGAGGGGCAGAAGTGCGACCACGTGGGGTCCACGGCGGTGGTGGCCGTCGTGGAGGAGAGCCGCGTCGTCGTGG
CCAACTGCGGCGATTCCCGCGCCGTGCTCTGCCGCGGCGGCGCGCCCGTGCAGCTCTCCTCCGACCACAAGCCCGACCGC
CCCGACGAGCTGGAGCGGATCGAGGAGGCCGGCGGCCGCGTCATCTTCTGGGAGGGCGCCAGGGTCCTCGGCGTCCTCGC
CATGTCGCGCTCCATCGGCGACGCCTACCTGAAGCCCTACGTCACCGCCGTGCCGGAGGTGACGGTGACCGGCAGGTCGG
ACGCCGACGAGTGCCTCATCCTCGCCAGCGACGGCCTCTGGGACGTCGTCAGCAACGAGGCCGCGTGCGAGGTGGCGCAG
TCGTGCCTCCGCCGCGGCAGGCAGCGGTGGTGCGCCGAGGCGGCGGCGGTGCTGACCAAGCTGGCCCTCGCTCGCCGCAG
CTCCGACAACATCTCCGTCGTCGTCGTCGATCTCCGGCGAGGCAATGCCTTGTAG

Alignment

ORF - retro_oglu_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.46 %
• Parental protein coverage: 75.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDAVSIRPDFLR---GSTSSGKHHFFGVFDGHGCSHVARMCQDRMHELVVD---AYKKAVSGKEAAAAA
          MEDAVS.R..F.....G........F.GVFDGHGCSHVA..C..RMHELV.....A...AV....AA...
Retrocopy MEDAVSLREAFAAPADGEVAAARCDFYGVFDGHGCSHVADACRERMHELVAEEMGAGSPAVAAAAAAREP

Parental  PAWKDVMEKGFARMDDEATIWAKSRTGGEPACRCELQTPARCDHVGSTAVVAVVGPNRVVVANSGDSRAV
          ..W..VME..FARMD.E.........G....CRCE.Q....CDHVGSTAVVAVV...RVVVAN.GDSRAV
Retrocopy ASWTGVMERSFARMDAEVIAGCRAESG---SCRCEGQ---KCDHVGSTAVVAVVEESRVVVANCGDSRAV

Parental  LCRAGVPVPLSVDHKPDRPDELERIKAAGGRVIYWDGARVLGVLAMSRAIGDGYLKPYVTSEPEVTVTER
          LCR.G.PV.LS.DHKPDRPDELERI..AGGRVI.W.GARVLGVLAMSR.IGD.YLKPYVT..PEVTVT.R
Retrocopy LCRGGAPVQLSSDHKPDRPDELERIEEAGGRVIFWEGARVLGVLAMSRSIGDAYLKPYVTAVPEVTVTGR

Parental  ADDDECLILASDGLWDVVTNEMACEVVRACFR
          .D.DECLILASDGLWDVV.NE.ACEV...C.R
Retrocopy SDADECLILASDGLWDVVSNEAACEVAQSCLR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza glumaepatula was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_4 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017925	1 retrocopy	retro_oind_21,
Oryza glumaepatula	OGLUM05G20150	1 retrocopy	retro_oglu_4 ,
Oryza meridionalis	OMERI05G16600	1 retrocopy	retro_omer_16,
Oryza nivara	ONIVA05G19940	1 retrocopy	retro_oniv_23,
Oryza glaberrima	ORGLA05G0165000	1 retrocopy	retro_ogla_36,
Oryza rufipogon	ORUFI05G20280	1 retrocopy	retro_oruf_40,