RetrogeneDB ID: retro_oana_47

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig216762:320..788(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A3
• Ensembl ID: ENSOANG00000000334
• Aliases: None
• Description: eukaryotic translation initiation factor 4A3 [Source:HGNC Symbol;Acc:18683]

Sequence

>retro_oana_47
CTTCAGGTTCACTGTTGCATTGGAGGGAAGAGAGTTTCTGATGATATTAGGGCGCTAGAGTCAGGAGTACAAATAGTTTC
CGGGACGCCTGGTAGAGTTAACCATATGATTTCACAACGGCACTTAAATACACGTAACATCAAGCAACTTATTTTGGACG
AGGCAGACGAAATGTTAAATCGCGGTTTCAAGGAACAAGTGTACTCTGTATATCGCTATCTACCCCCGACCATACAAGTG
GTTTTAGTGTCAGCAACACTGCCCCATGAAGTCATAGAAATAACGAACAAATTCATGAACAATCCCTTTAGAGTTCTCGT
CAAACGTGACGAATTGACATTGGAGGGAATTAAACAGTTTTTTGTATCAATAGAAAAGGAGCAGTGGAAATTTGACACTC
TCTGTGATCTCTACGAGTCGTTGATTATTACACAGGCCGTGGTATTTTGTAATACCAGGGAGAAGGTT

Alignment

ORF - retro_oana_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.51 %
• Parental protein coverage: 54.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDV
          .Q.H.CIGG..V..DIR.L..G...V.GTPGRV..MI..R.L.TR.IK.L.LDEADEMLN.GFKEQ.Y.V
Retrocopy LQVHCCIGGKRVSDDIRALESGVQIVSGTPGRVNHMISQRHLNTRNIKQLILDEADEMLNRGFKEQVYSV

Parental  YRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT
          YRYLPP..QVVL.SATLPHE..E.TNKFM..P.R.LVKRDELTLEGIKQFFV..E.E.WKFDTLCDLY..
Retrocopy YRYLPPTIQVVLVSATLPHEVIEITNKFMNNPFRVLVKRDELTLEGIKQFFVSIEKEQWKFDTLCDLYES

Parental  LTITQAVIFCNTKRKV
          L.ITQAV.FCNT..KV
Retrocopy LIITQAVVFCNTREKV

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	40.98 RPM
SRP007412_cerebellum	0.00 RPM	61.51 RPM
SRP007412_heart	0.00 RPM	50.92 RPM
SRP007412_kidney	0.00 RPM	33.46 RPM
SRP007412_liver	0.00 RPM	25.31 RPM
SRP007412_testis	0.00 RPM	63.57 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_47 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_47 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000009136	2 retrocopies	retro_mmur_444, retro_mmur_50,
Myotis lucifugus	ENSMLUG00000009585	1 retrocopy	retro_mluc_65,
Macaca mulatta	ENSMMUG00000009590	1 retrocopy	retro_mmul_851,
Monodelphis domestica	ENSMODG00000002190	1 retrocopy	retro_mdom_202,
Mus musculus	ENSMUSG00000025580	2 retrocopies	retro_mmus_2752, retro_mmus_70,
Ornithorhynchus anatinus	ENSOANG00000000334	1 retrocopy	retro_oana_47 ,
Otolemur garnettii	ENSOGAG00000007495	1 retrocopy	retro_ogar_212,