RetrogeneDB ID: retro_ogla_20

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 4:18485552..18486470(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA04G0163400
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA03G0142400
• Aliases: None
• Description: None

Sequence

>retro_ogla_20
ATGCTCCCCGTGGCCCCCGCTCGTCAGCCTCTAACCGCCTCGTCTTGGCCTCGCCTAGCCGCGGCGGGACCCACGCCGCC
CAGACCCAATCTCCCCCTAAACCCCGCACCGCCGCCGCCGAACCCTAGCCCCGCCGCCATGCTGCGCCGCCTCGCCGCCG
CCGCGCCGCGGGCCTTCTTCTCGTCGTCGACCCCGCACGCACCGCCGCCGCCGGCGGGGTACACCCAGCGCCGCGAGTAC
GGGCTGGTCCCCATGGTGATCGAGCACACCTCCCGCGGGGAGCGGGCGTACGACATCTTCTCGCGCCTCCTCAAGGAGCG
GATCGTCTGCATCCACGGGCCAATCACCGACGACACGGCCTCCCTCGTCGTCGCCCAGCTGCTCTTCCTCGAGTCCGAGA
ACCCCGCCAAGCCCGTCCACCTCTACATCAACTCCCCCGGCGGGGTCGTCACCGCGGGCCTCGCGATCTACGACACCATG
CAGTACATCCGCTCCCCGGTCACCACGCTCTGCATCGGCCAGGCCGCGTCCATGGCCTCGCTCCTCCTCGCCGCGGGCGC
GCGCGGCGAGCGGCGGGCGCTCCCCAACGCGCGCGTCATGATCCACCAGCCGTCGGGCGGCGCGTCGGGGCAGGCGTCCG
ACATCGCCATCCACGCCAAGGAGATCCTCAAGGTGCGCGACCGTCTCAACAAGATCTACGCGAAGCACACGAGCCAGGCC
ATCGACCGTATCGAGCAGTGCATGGAGCGGGACATGTTCATGGATCCAGAGGAGGCGCACGACTGGGGGCTCATCGACGA
GGTCATCGAGCACCGCCCAGTTTCACTGGTTTCTGATGCCGTCGGCAGCGATCTGCCAAACCTAGGCGGGGGCGGAGATG
GGGCTAACAAGGCAACTGATGAACCATCTCCAGCTTGA

Alignment

ORF - retro_ogla_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.14 %
• Parental protein coverage: 62.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERFQSVVSQLFQHRIIRCGGPVEDDMANIIVAQLLYLDAIDPNKDIIMYVNSPGGSVTAGMAIFDTMKHI
          ER.....S.L...RI....GP..DD.A...VAQLL.L....P.K....Y.NSPGG.VTAG.AI.DTM..I
Retrocopy ERAYDIFSRLLKERIVCIHGPITDDTASLVVAQLLFLESENPAKPVHLYINSPGGVVTAGLAIYDTMQYI

Parental  RPDVSTVCIGLAASMGAFLLSAGTKGKRYSLPNSRIMIHQPLGGAQGQETDLEIQANEMLHHKANLNGYL
          R..V.T.CIG.AASM...LL.AG..G.R..LPN.R.MIHQP.GGA.GQ..D..I.A.E.L.....LN...
Retrocopy RSPVTTLCIGQAASMASLLLAAGARGERRALPNARVMIHQPSGGASGQASDIAIHAKEILKVRDRLNKIY

Parental  AYHTGQPLDKINVDTDRDYFMSAKEAKEYGLIDGVI
          A.HT.Q..D.I.....RD.FM...EA...GLID.VI
Retrocopy AKHTSQAIDRIEQCMERDMFMDPEEAHDWGLIDEVI

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_20 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00045p00165520	1 retrocopy	retro_atri_13,
Oryza brachyantha	OB03G24650	1 retrocopy	retro_obra_19,
Oryza glaberrima	ORGLA03G0142400	1 retrocopy	retro_ogla_20 ,
Triticum aestivum	Traes_4AS_C67AE6944	1 retrocopy	retro_taes_83,