RetrogeneDB ID: retro_oglu_16

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 3:37389696..37390434(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM03G41500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM04G18920
• Aliases: None
• Description: None

Sequence

>retro_oglu_16
ATGGAGAATAGCAGGGAGCAGCAGCCGGAGTCGTCGCCGGCGAACAACAATAGCAAGAAGAAGAAGAAGAAGAAGAAGAC
GGCGTCGCGGTTCCGGCGTGTGTGCGTGTTCTGCGGCAGCAGCCCCGGGAAGAAGGCGTCGTACCAGGTGGCCGCCGTGC
AGCTGGGGCAGCAGCTGGTGGAGCGCCGCATCGACCTGGTGTACGGCGGCGGCAGCGTTGGGCTGATGGGGCTGGTGTCC
CGCGCCGTCCACGGAGGCGGCGGGCACGTGGTGGGCGTGGTGCCCAATGGCGTGCTGCCACGCGAGCTGATCGGCGAGAC
GCTGGGGGAGGTGAGGGCGGTGGGAAGCATGCACCAGCGGAAGGCGGAGATGGCGCGGGAGTCGGACGCCTTCATCGCCC
TCCCCGGCGGCTACGGCACGCTGGAGGAGCTCCTGGAGGTCATCACCTGGGCTCAGCTCCGCATCCACCACAAGCCCGTC
GGCCTCCTCAACGTCGACGGCTACTACGACTCCCTGCTCGCCTTCATCGACAAGGCCGTCCACGAAGGCTTCGTCTCGCC
GCCCGCCCGCCGCATCATCGTCGCCGCGCCCACCGCCTCCGACCTGCTCTGCAAGCTCGAGGAATACGTGCCGCCGCCGC
ACGACGCCACCGCCCTGAAGCTCACCTGGGAGATGTCCACCGTATCGGAGCAGCACGCCGGAAGCATCTACTCCCCCAAG
CCCGACATGGCACGCTAG

Alignment

ORF - retro_oglu_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRFRRICVFCGSSQGKKKSYQDAAVELGKELVARNIDLVYGGGSVGLMGLVSQAVYNGGRHVIGVIPKTL
          SRFRR.CVFCGSS.GKK.SYQ.AAV.LG..LV.R.IDLVYGGGSVGLMGLVS.AV..GG.HV.GV.P...
Retrocopy SRFRRVCVFCGSSPGKKASYQVAAVQLGQQLVERRIDLVYGGGSVGLMGLVSRAVHGGGGHVVGVVPNGV

Parental  MPREITGETVGEVKAVADMHQRKAEMARQSDAFIALPGGYGTLEELLEVIAWAQLGIHDKPVGLLNVDGY
          .PRE..GET.GEV.AV..MHQRKAEMAR.SDAFIALPGGYGTLEELLEVI.WAQL.IH.KPVGLLNVDGY
Retrocopy LPRELIGETLGEVRAVGSMHQRKAEMARESDAFIALPGGYGTLEELLEVITWAQLRIHHKPVGLLNVDGY

Parental  YNSLLSFIDKAVEEEFISPSARHIIVLAPTPKELLEKLEAY-SPRHDKVVPKMQWEMEKMS
          Y.SLL.FIDKAV.E.F.SP.AR.IIV.APT...LL.KLE.Y..P.HD....K..WEM...S
Retrocopy YDSLLAFIDKAVHEGFVSPPARRIIVAAPTASDLLCKLEEYVPPPHDATALKLTWEMSTVS

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_16 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_6463	1 retrocopy	retro_hvul_10,
Oryza glumaepatula	OGLUM04G18920	1 retrocopy	retro_oglu_16 ,