RetrogeneDB ID: retro_oana_94

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig78472:3408..3669(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB6B
• Ensembl ID: ENSOANG00000031623
• Aliases: None
• Description: RAB6B, member RAS oncogene family [Source:HGNC Symbol;Acc:14902]

Sequence

>retro_oana_94
GGGAAAACCTCCATTGTTACGAGATTTGTTTATGATCATTTTGTGCCAACGTACCAAGCAACCATTGGAATTGATTTTCT
CAGCAAAGTAGTGCACGTTAACCAAAAAACCATGCGCCTTCAGCTCTGGGACACTGCTGGCCAGGAGAGATTTCGCAGTT
TGATGCCCAGCTACATTAGGGACAGTTCGGCTGCTATTGTGGTTTATGATATAACCAACAGGGAGTCATTTGTGAATACC
AAGCAGTGGATTCAGGATGTT

Alignment

ORF - retro_oana_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 69.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYD
          GKTS..TRF.YD.F..TYQATIGIDFLSK.......T.RLQLWDTAGQERFRSL.PSYIRDS..A.VVYD
Retrocopy GKTSIVTRFVYDHFVPTYQATIGIDFLSKVVHVNQKTMRLQLWDTAGQERFRSLMPSYIRDSSAAIVVYD

Parental  ITNLNSFQQTSKWIDDV
          ITN..SF..T..WI.DV
Retrocopy ITNRESFVNTKQWIQDV

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	41.33 RPM
SRP007412_cerebellum	0.00 RPM	31.83 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.09 RPM
SRP007412_testis	0.00 RPM	0.71 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_94 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_94 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009412	1 retrocopy	retro_etel_1486,
Loxodonta africana	ENSLAFG00000009905	1 retrocopy	retro_lafr_430,
Ornithorhynchus anatinus	ENSOANG00000031623	1 retrocopy	retro_oana_94 ,
Ochotona princeps	ENSOPRG00000001164	5 retrocopies	retro_opri_1098, retro_opri_20, retro_opri_606, retro_opri_797, retro_opri_993,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,