RetrogeneDB ID: retro_oana_10

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: 7:23133265..23133748(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOANG00000012950
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TWIST1
• Ensembl ID: ENSOANG00000009614
• Aliases: None
• Description: twist basic helix-loop-helix transcription factor 1 [Source:HGNC Symbol;Acc:12428]

Sequence

>retro_oana_10
ATGGAGGAAAGTTCCAGTTCTCCTGTCTCTCCTGTGGATAGCTTGGGAACCAGCGAAGAAGAGCTCGAGAGACAGCCAAA
AAGATTTGGCAGGAAAAGAAGATACAGTAAGAAATCCAGTGAAGATGGCAGCCCCAATCCTGGAAAACGGGGTAAGAAGG
CCAGTCCCAGCTCCCAGTCTTATGAAGAACTTCAAAGCCAGAGGATCCTGGCCAATGTCAGGGAGAGGCAGAGGACGCAA
TCCCTCAATGAAGCATTTGCAGCCCTGAGGAAAATCATCCCCACCCTACCCTCGGACAAACTCAGTAAAATTCAGACTCT
CAAGCTTGCAGCCAGGTATATAGACTTCCTCTACCAGGTCCTCCAGAGCGACGAAATGGACAATAAGATGACAAGTTGCA
GCTATGTAGCCCATGAGAGACTCAGTTATGCCTTTTCCGTGTGGAGGATGGAAGGAGCATGGTCCATGTCGGCATCCCAC
TAG

Alignment

ORF - retro_oana_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQDASSSPVSPADDSLSNSDEEQDRPPPPGGKRGARKRRSSRRSDEPGSPAQGKRGKNGGGSPQSYEELQ
          M...SSSPVSP.D.SL..S.EE..R.P....KR..RKRR.S..S.E.GSP..GKRGK....S.QSYEELQ
Retrocopy MEESSSSPVSPVD-SLGTSEEELERQP----KRFGRKRRYSKKSSEDGSPNPGKRGKKASPSSQSYEELQ

Parental  TQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQSDELDSKMASCSY
          .QR..ANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQSDE.D.KM.SCSY
Retrocopy SQRILANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQSDEMDNKMTSCSY

Parental  VAHERLSYAFSVWRME
          VAHERLSYAFSVWRME
Retrocopy VAHERLSYAFSVWRME

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	2.12 RPM	0.18 RPM
SRP007412_cerebellum	0.28 RPM	0.19 RPM
SRP007412_heart	0.18 RPM	0.18 RPM
SRP007412_kidney	0.30 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.18 RPM
SRP007412_testis	0.12 RPM	0.12 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_10 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_10 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000023924	1 retrocopy	retro_mdom_15,
Ornithorhynchus anatinus	ENSOANG00000009614	1 retrocopy	retro_oana_10 ,