RetrogeneDB ID: retro_mdom_542

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:229075222..229075852(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: INSIG2
• Ensembl ID: ENSMODG00000000458
• Aliases: None
• Description: insulin induced gene 2 [Source:HGNC Symbol;Acc:20452]

Sequence

>retro_mdom_542
GAGAGAGAGACAGCATCATCTGTACCCCCAAAGTGTGGGCCATACATTTCTTCTGTCACTAGTTGGAGTATGAACTTGAT
GATTCGTGGAGTAGTTCTGTTTTTGATTGGAGTGTTTCTTGCTCTAGTATTAAATCTACATCAGATTCAGAGAAATGTCA
CACTCCTTCCACCAGATGTGATTGCAAGCATCTTTTCTTCAGCATGGTGGTTGCCACCATGCTGTGGCACAGCTTCAGCT
GTGATTAGGTTGTTATACCCTTGCATTGACAGGCATCTGGGAGAGTCACATGAATTTAAAAGAGAGTGTTCTAGTGTAAT
GCGATGTGTAGCAGTCTTTGTTGGTATTAATCATGCCAGTGCTAAAGTAGATTTTGACAACAATATACAGTTGTCTCTCA
CTCTAGCTGCACTATCCATTGGCTTGTGGTGGACTTTTGATAGATCACGAAGTGGTTTTGGTCTTGGAGTAGGAATTGCT
TTCTTGGCAACCTTGGTCACTCAACTACTAGTCTACAATGGGGTTTATCAGTATACATCTCCAGATTTTCTTTATGTCTG
TTCTTGGTTACCATGTATATTTTTTGCTGGTGGCAAAACAATGGGAAATATTGATCGACAACTGGCCATG

Alignment

ORF - retro_mdom_542 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.76 %
• Parental protein coverage: 98.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERETASSVPPKCGPYISSVTSRSMNLMIRGVVLFLIGVFLALVLNLLQIQRNVTLFPPDVIASIFSSAWW
          ERETASSVPPKCGPYISSVTS.SMNLMIRGVVLFLIGVFLALVLNL.QIQRNVTL.PPDVIASIFSSAWW
Retrocopy ERETASSVPPKCGPYISSVTSWSMNLMIRGVVLFLIGVFLALVLNLHQIQRNVTLLPPDVIASIFSSAWW

Parental  VPPCCGTASAVIGLLYPCIDRHLGEPHKFKREWSSVMRCVAVFVGINHASAKVDFDNNIQLSLTLAALSI
          .PPCCGTASAVI.LLYPCIDRHLGE.H.FKRE.SSVMRCVAVFVGINHASAKVDFDNNIQLSLTLAALSI
Retrocopy LPPCCGTASAVIRLLYPCIDRHLGESHEFKRECSSVMRCVAVFVGINHASAKVDFDNNIQLSLTLAALSI

Parental  GLWWTFDRSRSGFGLGVGIAFLATLVTQLLVYNGVYQYTSPDFLYVRSWLPCIFFAGGITMGNIGRQLAM
          GLWWTFDRSRSGFGLGVGIAFLATLVTQLLVYNGVYQYTSPDFLYV.SWLPCIFFAGG.TMGNI.RQLAM
Retrocopy GLWWTFDRSRSGFGLGVGIAFLATLVTQLLVYNGVYQYTSPDFLYVCSWLPCIFFAGGKTMGNIDRQLAM

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	0.48 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.80 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	1.38 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_542 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_542 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008765	1 retrocopy	retro_eeur_508,
Myotis lucifugus	ENSMLUG00000028113	1 retrocopy	retro_mluc_2270,
Macaca mulatta	ENSMMUG00000006354	1 retrocopy	retro_mmul_703,
Monodelphis domestica	ENSMODG00000000458	2 retrocopies	retro_mdom_1872, retro_mdom_542 ,
Otolemur garnettii	ENSOGAG00000007739	1 retrocopy	retro_ogar_940,