RetrogeneDB ID: retro_obar_35

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 9:11994936..11995158(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART01G15350
• Aliases: None
• Description: None

Sequence

>retro_obar_35
ATTCGGTTTCCAATCTTCGGTCGTTCTGTTTGCGTCGGTTTCCAAACTTTGGTCCGATTTACGTGGAACATATCATATTC
TCATGATCTTGATAATTATTTCCAGTTAGTCATTAATTTACATAGCAATTTGGTGATCCATCTTTTGATGAATGTAATCA
AAGATTGAAAGGACAACAAATTGAGAAGATTTACGCACCTAACAAGAACAAAACAAGTTCAA

Alignment

ORF - retro_obar_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.35 %
• Parental protein coverage: 92.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEHPIFSANCLKMLRAPTNLVQSLLWEPGMECTREKVINFHSNLVIHRLMNVIKDRKDNKLRRFTHLTRT
          ...PIF..............................VIN.HSNLVIH.LMNVIKD.KDNKLRRFTHLTRT
Retrocopy IRFPIFGRSVCVGFQTLVRFTWNISYSHDLDNYFQLVINLHSNLVIHLLMNVIKD*KDNKLRRFTHLTRT

Parental  KQVQ
          KQVQ
Retrocopy KQVQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza barthii was not studied using ChIP-Seq data.

EST

Oryza barthii was not studied using EST data.

TSS

Oryza barthii was not studied using FANTOM5 data.

Lab

retro_obar_35 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza barthii 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 barthii	OBART01G15350	1 retrocopy	retro_obar_35 ,