RetrogeneDB ID: retro_oglu_14

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 12:13917685..13918312(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM12G11380
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM08G07940
• Aliases: None
• Description: None

Sequence

>retro_oglu_14
ATGCTCCAGCTCGACGGCGGCGAAAACGCGTCGGACCTGTTCAACCTGCACCGCCCGGTGATCACCGGAGTCCCCCACGA
CGTGGCGTCAGCGCTCAACACCCTGGAGGAGATCCTCTCCAGAGGGAGCCCGACGCTGGAAGCGTACCAGCGAGAGGACA
TCCGGGAGACGAGGGTGCTCCAGGAGGAGAAGGTCCGGACCACCATGGCCGAGGTGCGTTACATCGACGGGCTCGTCGAT
GAGCACATGGATGCTGTCGAAGGGACCAGGGTCCGCCTCCACGCGGCCCGCGACATCAAGCAGCAGCTGCTCGAAAAGAT
CACCGCAGCGGCAGCGGACGGCGGCGAACAAACCGTCGACGTCGCATCCCTGGAGCTGGAGCTCAGCGAGGCGGAGGAGA
GTGAGGCCGCGCTGTTGGCCGAGTTTATGAACCAGTGGCAGTCAGTGCTCGCCGTGCACAAGCACCGTGGGGTCGCCAAG
AGCCGATTCGAAGACGAGGTGGTGGCCCTCATGGCCATCCCACAGCTGCCTGGTCACTCCGAAGATCAACACCTCGTTGG
AGATGCGGAGGAGCGCTACGAGGACAGTGTTCTCCTGCTCGACGAGTTCTTGGACATGCAATACTAA

Alignment

ORF - retro_oglu_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 97.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVASDLFSLQCPMITGGSPTLVAYQREDIRERSALQEEKVRATMAEVRYFDGLVDEHMDAIEGTRARLHA
          DVAS.L..L.......GSPTL.AYQREDIRE...LQEEKVR.TMAEVRY.DGLVDEHMDA.EGTR.RLHA
Retrocopy DVASALNTLE-EILSRGSPTLEAYQREDIRETRVLQEEKVRTTMAEVRYIDGLVDEHMDAVEGTRVRLHA

Parental  TRSTKQQMLSMLTAAEAAAADGTGEAAAITSLELELDEAEDREAVLEAEFMRLWPLVLTPNKHRVRGVAK
          .R..KQQ.L...TAA...AADG........SLELEL.EAE..EA.L.AEFM..W..VL...KH..RGVAK
Retrocopy ARDIKQQLLEKITAA---AADGGEQTVDVASLELELSEAEESEAALLAEFMNQWQSVLAVHKH--RGVAK

Parental  SRSEDGVKVLMAILELPGRSEGEHLIGDAEERYDDRVLLLDKFLDM
          SR.ED.V..LMAI..LPG.SE..HL.GDAEERY.D.VLLLD.FLDM
Retrocopy SRFEDEVVALMAIPQLPGHSEDQHLVGDAEERYEDSVLLLDEFLDM

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_14 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM08G07940	1 retrocopy	retro_oglu_14 ,