RetrogeneDB ID: retro_oana_40

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig185460:492..836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ox_plat1_467209
• Ensembl ID: ENSOANG00000020682
• Aliases: None
• Description: None

Sequence

>retro_oana_40
ATGCTCACTCTTCATAATGCCAACATAAACCTTTCAGTAATTGGTCTGAAGGCATTAGATCTTCTTCTGACTTCAGATGT
GATGACTCTGTTGGTTTTGGATGAAGAAAGTAATGTATTTTTGTTAATTTTTGATGCTATGCATACCTTCCCATCTAATG
AAGAAGTTCAAAGATTTGGATGTAAAGCTTTACATGTGCTTTTTGAAAGAGTTCCAGAAGAGCAACTGACTGAGTTTTTT
GAGAGCAAAGATCATATGATTGTGTTGGATGCATAAAACAATTTAAAAATAAAGAGGAAGTGGTGTTTCATGCACTTCAC
TGCTTACACTCATTGGCAGTTCCA

Alignment

ORF - retro_oana_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 52.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLTLHNANINLSVIG-KALDLLLTSDVMTLLVLDEESDVFLLIFDA-HTFPSNEEVQRFGCKALH-LFER
          MLTLHNANINLSVIG.KALDLLLTSDVMTLLVLDEES.VFLLIFDA.HTFPSNEEVQRFGCKALH.LFER
Retrocopy MLTLHNANINLSVIGLKALDLLLTSDVMTLLVLDEESNVFLLIFDAMHTFPSNEEVQRFGCKALHVLFER

Parental  -PEEQLTEFFESKDHMIVLDA-LKQFKNKEEVVFHALHCLHSLAVP
          .PEEQLTEFFESKDHMIVLDA..KQFKNKEEVVFHALHCLHSLAVP
Retrocopy VPEEQLTEFFESKDHMIVLDA<IKQFKNKEEVVFHALHCLHSLAVP

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	0.35 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.27 RPM
SRP007412_kidney	0.00 RPM	0.59 RPM
SRP007412_liver	0.00 RPM	0.09 RPM
SRP007412_testis	0.00 RPM	0.83 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_40 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_40 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	ENSOANG00000020682	1 retrocopy	retro_oana_40 ,