RetrogeneDB ID: retro_mdom_15

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:531405873..531406359(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000001412
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TWIST1
• Ensembl ID: ENSMODG00000023924
• Aliases: None
• Description: twist basic helix-loop-helix transcription factor 1 [Source:HGNC Symbol;Acc:12428]

Sequence

>retro_mdom_15
AGAATGGAGGAAGGCTCCAGTTCTCCGGTCTCGCCGGTGGACAGCTTGGGCACCAGCGAAGAGGAGCTGGAAAGGCAGCC
CAAGAGGTTTGGCAGAAAGAGAAGGTACAGCAAGAAATCCAGCGAAGATGGCAGCCCCACCCCGGGCAAGCGGGGGAAGA
AGGGCAGCCCCAGCTCGCAGTCCTATGAGGAGCTGCAGAGCCAGAGGATTCTGGCCAACGTCCGGGAGAGGCAGAGGACG
CAGTCCCTGAACGAAGCCTTCGCCGCCCTGCGCAAGATCATCCCCACTCTGCCCTCCGACAAACTCAGCAAGATCCAGAC
CCTGAAGCTGGCAGCCAGGTACATAGACTTCCTCTACCAGGTGCTGCAGAGCGACGAGATGGACAATAAGATGACCAGCT
GCAGCTACGTGGCCCACGAGAGGCTCAGCTATGCCTTTTCCGTGTGGAGGATGGAGGGCGCGTGGTCCATGTCGGCATCC
CACTAG

Alignment

ORF - retro_mdom_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.52 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEEEPDRQQSSVGGKRGGRKRRRSRGRPGQSSPRQAGQ---ESYEELQTQRVMANVRERQRTQSLNEAFA
          SEEE..RQ....G.KR...K.....G.P........G.....SYEELQ.QR..ANVRERQRTQSLNEAFA
Retrocopy SEEELERQPKRFGRKRRYSKKSSEDGSPTPGKRGKKGSPSSQSYEELQSQRILANVRERQRTQSLNEAFA

Parental  ALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQSDELDSKMASCSYVAHERLSYAFSVWRMEGAWSMS
          ALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQSDE.D.KM.SCSYVAHERLSYAFSVWRMEGAWSMS
Retrocopy ALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQSDEMDNKMTSCSYVAHERLSYAFSVWRMEGAWSMS

Parental  ASH
          ASH
Retrocopy ASH

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_15 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_15 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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,