RetrogeneDB ID: retro_oana_28

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig11843:28255..28543(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TGFA
• Ensembl ID: ENSOANG00000010070
• Aliases: None
• Description: transforming growth factor, alpha [Source:HGNC Symbol;Acc:11765]

Sequence

>retro_oana_28
GCTGCCTGCCAGGCCCTGGAGAGTACATTGGCCTTGAGTGGCGCCCCTGTGACCGCGGCCGTCCAGTCCCATTTCGACGA
GTGCCCAGATTCTCAGAGTCAGTTCTGCTTCCACAGCACCTGCAGATTCTTGGTTCAGGAGGACAAGTCGGCATGTGTGA
GCCACTCGGGGTTCGTGGGAGTGCGGTGTGAGCACGCAGGCCCGCTGGTCGTGGTGACGGCCATGCAGAAGAAGCAGACC
ATCACCGCCCTGCTTGTGGTGTCCGCTGGGGCCTCCATTACCCTGGCA

Alignment

ORF - retro_oana_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.71 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STCLVLWSVSPFTGAPVPAAVRSHFNECPDSHSQFCFHGTCRFLVEENKPACKCHLGFMGERCEHADLLA
          ..C..L.S.....GAPV.AAV.SHF.ECPDS.SQFCFH.TCRFLV.E.K.AC..H.GF.G.RCEHA..L.
Retrocopy AACQALESTLALSGAPVTAAVQSHFDECPDSQSQFCFHSTCRFLVQEDKSACVSHSGFVGVRCEHAGPLV

Parental  VVAATQKKQTITALLVVSVLASVTLA
          VV.A.QKKQTITALLVVS..AS.TLA
Retrocopy VVTAMQKKQTITALLVVSAGASITLA

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	0.79 RPM
SRP007412_cerebellum	0.00 RPM	2.25 RPM
SRP007412_heart	0.00 RPM	2.13 RPM
SRP007412_kidney	0.00 RPM	0.30 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.36 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_28 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_28 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ornithorhynchus anatinus	ENSOANG00000010070	1 retrocopy	retro_oana_28 ,