RetrogeneDB ID: retro_oglu_31

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 1:42667469..42668585(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM01G45300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM05G09560
• Aliases: None
• Description: None

Sequence

>retro_oglu_31
ATGGGGAGGGTTATTAGCAGCTGGAGGGTTCTTGCGGTGGTGGCTGCTTTGATGGCCATGGCGGCGGTGGAGCTGTGCGC
CGCGATACCGTTCGACGAGAGGGATTTGGAGTCCGACGAGGCGCTGTGGGATCTGTACGAGCGGTGGCAGGAGCACCACC
ACGTGCCGCGCCACCACGGCGAGAAGCACCGCCGGTTCGGCGCGTTCAAGGACAACGTGAGGTACATCCACGAGCACAAC
AAGCGCGGCGGCCGGGGCTACCGCCTCCGGCTCAACCGCTTCGGCGACATGGGCAGGGATGAGTTCCGCGCCACGTTCGC
CGGGTCCCACGCCAACGACCTCCGCCGCGACGGCCTCGCCGCGCCGCCGCTCCCGGGGTTCATGTACGAGGGCGTCCGCG
ACCTCCCCCGCGCCGTCGACTGGCGCCGCAAGGGCGCGGTCACCGGCGTCAAGGACCAGGGCAAGTGCGGCAGCTGCTGG
GCGTTCTCCACGGTGGTGTCCGTGGAGGGCATCAACGCGATCCGGACGGGGCGGCTGGTGTCGCTGTCGGAGCAGGAGCT
GATCGACTGCGACACGGCGGACAACAGCGGCTGCCAGGGCGGGCTCATGGAGAACGCGTTCGAGTACATCAAGCACAGCG
GCGGCATCACCACCGAGTCCGCCTACCCGTACCGCGCCGCCAACGGAACGTGCGACGCCGTCCGCGCGCGGCGCGCGCCG
CTGGTGGTGATCGACGGGCACCAGAACGTGCCGGCCAACAGCGAGGCCGCGCTCGCCAAGGCCGTCGCCAACCAGCCCGT
CTCCGTCGCCATCGACGCCGGCGACCAGTCCTTCCAGTTCTACTCCGACGGCGTCTTCACCGGCGACTGCGGCACCGACC
TCGACCACGGCGTCGCGGTGGTCGGCTACGGCGAGACCAACGACGGCACGGAATACTGGATCGTCAAGAACTCGTGGGGC
ACAGCCTGGGGCGAGGGCGGCTACATCCGGATGCAGCGCGACTCCGGCTACGACGGCGGCCTCTGCGGCATCGCCATGGA
AGCCTCCTACCCCGTCAAGTTCTCGCCAAATCGTGTCACGCCAAGGCGCGCCCTTGGCGCCAAGGAAACCCAGTGA

Alignment

ORF - retro_oglu_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 52.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLPPAVDWRERGAVTGIKDQGQCGSCWAFSAVAAVEGVNKIKTGRLVALSEQELVDCDTGDNQGCDGGLM
          .LP.AVDWR..GAVTG.KDQG.CGSCWAFS.V..VEG.N.I.TGRLV.LSEQEL.DCDT.DN.GC.GGLM
Retrocopy DLPRAVDWRRKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGRLVSLSEQELIDCDTADNSGCQGGLM

Parental  DYAFQFIKRNGGITTESNYPYRAEQGRCNKAKASSHD-VTIDGYEDVPANDELALQKAVANQPVAVAIEA
          ..AF..IK..GGITTES.YPYRA..G.C....A.....V.IDG...VPAN.E.AL.KAVANQPV.VAI.A
Retrocopy ENAFEYIKHSGGITTESAYPYRAANGTCDAVRARRAPLVVIDGHQNVPANSEAALAKAVANQPVSVAIDA

Parental  SGQDFQFYSEGVFTGECGTDLDHGVAAVGYGITRDGTKYWIVKNSWGEDWGERGYIRMQRGVSSGSNGLC
          ..Q.FQFYS.GVFTG.CGTDLDHGVA.VGYG.T.DGT.YWIVKNSWG..WGE.GYIRMQR..S....GLC
Retrocopy GDQSFQFYSDGVFTGDCGTDLDHGVAVVGYGETNDGTEYWIVKNSWGTAWGEGGYIRMQRD-SGYDGGLC

Parental  GIAMEASYPVK
          GIAMEASYPVK
Retrocopy GIAMEASYPVK

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_31 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31 ,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27,