RetrogeneDB ID: retro_oana_23

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: 7:22279412..22280090(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000003153
• Aliases: None
• Description: None

Sequence

>retro_oana_23
ATGGGTAAGAAGAGCCGAGTGAAAACTCAGAAATCAGGTACCGGAGCTACAGCAACAGTATCACCAAAGGAAATGTTGGA
TCTAATTAGTGAACTATTACAGAAATGCAGCAGCCCAACCCCTGGCCCTGGAAAGGAATGGGAAGAGTATGTGCAGATTC
GTGCCCTTGTTGAAAAAATACGGAAAAAGCAAAAAGGGCTGTCAGTTACTTTTGATGGAAAAAGAGAAGATTATTTCCCT
GATCTGATGAAATGGGCCACTGCAAATGGAGCATCCACGGAGGGGTTTGAATTGGTTAACTTTGAAGAGGGTTTTGGTCT
CAGAGCAACAAGGGAAATAAAGACAGAAGAACTGTTCCTGTGGGTTCCAAGAAAATTGCTGATGACAGTTGAATCAGCTA
AAAATTCAGTGTTGGGGTCCTTATATTCTCAAGACCGAATCCTTCAGGCTATGGGGAACATCACATTGGCATTTCATCTT
CTTTGTGAACGAGCCAACCCTAGCTCTTTCTGGCTGCCGTACATACAGACTCTCCCTAGCGAATATGATACTCCTCTCTA
TTTTGAAGAAGACGAAGTGCAGTATCTTCAGTCAACACAGGCCATCCATGATGTCTTCAGCCAGTACAAAAATACAGCTC
GACAATATGCCTATTTCTACAAAGTTATTCAGACCAAT

Alignment

ORF - retro_oana_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.23 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKKSRVKTQKSGTGATATVSPKEMLNLISELLQKCSSPTPGPGKEWEEYVQIRALVEKIRKKQKGLSVT
          MGKKSRVKTQKSGTGATATVSPKEML.LISELLQKCSSPTPGPGKEWEEYVQIRALVEKIRKKQKGLSVT
Retrocopy MGKKSRVKTQKSGTGATATVSPKEMLDLISELLQKCSSPTPGPGKEWEEYVQIRALVEKIRKKQKGLSVT

Parental  FDGKREDYFPDLMKWATANGASTEGFELVNFEEGFGLRATREIKAEELFLWVPRKLLMTVESAKNSVLGS
          FDGKREDYFPDLMKWATANGASTEGFELVNFEEGFGLRATREIK.EELFLWVPRKLLMTVESAKNSVLGS
Retrocopy FDGKREDYFPDLMKWATANGASTEGFELVNFEEGFGLRATREIKTEELFLWVPRKLLMTVESAKNSVLGS

Parental  LYSQDRILQAMGNITLAFHLLCERANPSSFWLPYIQTLPSEYDTPLYFEEDEVQYLQSTQAIHDVFSQYK
          LYSQDRILQAMGNITLAFHLLCERANPSSFWLPYIQTLPSEYDTPLYFEEDEVQYLQSTQAIHDVFSQYK
Retrocopy LYSQDRILQAMGNITLAFHLLCERANPSSFWLPYIQTLPSEYDTPLYFEEDEVQYLQSTQAIHDVFSQYK

Parental  NTARQYAYFYKVIQVS
          NTARQYAYFYKVIQ..
Retrocopy NTARQYAYFYKVIQTN

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	3.18 RPM	11.30 RPM
SRP007412_cerebellum	2.25 RPM	6.83 RPM
SRP007412_heart	0.44 RPM	2.39 RPM
SRP007412_kidney	4.74 RPM	12.44 RPM
SRP007412_liver	1.27 RPM	3.98 RPM
SRP007412_testis	1.90 RPM	3.91 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_23 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_23 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000056770	2 retrocopies	retro_mmus_1971, retro_mmus_305,
Ornithorhynchus anatinus	ENSOANG00000003153	1 retrocopy	retro_oana_23 ,