RetrogeneDB ID: retro_ogla_53

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 10:2225444..2225827(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA04G0104200
• Aliases: None
• Description: None

Sequence

>retro_ogla_53
TGGTGCGAGGACCGCTGCGTTATTGCTGTAGTTGTACCTCGACCATCTGAGGTTGCGGTGCAAGAGATTGCTACGTACTA
GTTCGAGGACCAGCGGACGAGTAGAATTATCTCTCGAACACCAATGGAAGCTGCGGTGTGAGAGATTGCTACGTACTGGT
TCGAGGACAAGCGAGCGTGTAGAATTATCTCTCGAACACCAATAGAGTGCTAGAGTTGGTTTATTACATGTGCGTCTCAT
GTGGCCAGCATGACTCACACACCTAACTTGTAGCATATCCGGATGTCCGTTCGCAATCATGTCGGGTGATCAAGCCGACG
GCGTTCGCGAGGAATTATCCGTTAACAACCTTTTCTCGAGTAGTCCAGCCGTGGCCGATGCTA

Alignment

ORF - retro_ogla_53 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 67.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WFENQRASRIISRTPMEIAVREITTYWFENQRASRIISRTPMEIAVREITTYWFENQRRTCRIISRTPIE
          W.E...........P.E.AV.EI.TY.FE.QR.SRIISRTPME.AV.EI.TYWFE...R.CRIISRTPIE
Retrocopy WCEDRCVIAVVVPRPSEVAVQEIATY*FEDQRTSRIISRTPMEAAV*EIATYWFED-KRACRIISRTPIE

Parental  -VLELVYYKCVSCGQHDSHTQLVAYPDVRSQSCRVIKPTAFARNYPLTTFSRVVQPWPVL
          .VLELVYY.CVSCGQHDSHT.LVAYPDVRSQSCRVIKPTAFARNYPLTTFSRVVQPWP.L
Retrocopy <VLELVYYMCVSCGQHDSHT*LVAYPDVRSQSCRVIKPTAFARNYPLTTFSRVVQPWPML

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_53 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA04G0104200	12 retrocopies	retro_ogla_48, retro_ogla_49, retro_ogla_50, retro_ogla_53 , retro_ogla_55, retro_ogla_56, retro_ogla_57, retro_ogla_58, retro_ogla_67, retro_ogla_68, retro_ogla_69, retro_ogla_72,