RetrogeneDB ID: retro_mdom_1872

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:171784881..171785289(+)
• Located in intron of: None

Retrocopy information

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

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_1872
TGCCATGCTTCAGCTTCAGCTGTGATTGGGTTATTATACCCCTGCATTGACAGGCATCTGGGAGAGCTACATAAATTTAA
GAGAGTGGTCCAGTGTATTGCCATGTGTAGCAATCTTTGTTGGTATAAATCATGGCAGTGCTAAAGTAGATTCTGACAAC
AATATACAGTTGTCTCTCACTCTAGCTGCACTATCCATTGACTTGGGGTGGACTTTTGATAGTTCACAAAATGGTTTTAG
CCTTGGAGTAGGAATTGCTTTATTGGCAACCTTGGTGGCTCAACTACTAGTCTATAATGGGGTTTATCAATACAGATCTT
CAGATTTTCTTTATGTCCATTCTTGGTTACCATGTATATTTTTTGCTGCTGGTATAACAATGGGAAATATTGGTAACAAC
TGGCTATG

Alignment

ORF - retro_mdom_1872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 64.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CCGTASAV-IGLLYPCIDRHLGEPHKFKREWSSVMRCVAVFVGINHASAKVDFDNNIQLSLTLAALSIGL
          C...ASAV..G...P.......E.....REWSSV..CVA.FVGINH.SAKVD.DNNIQLSLTLAALSI.L
Retrocopy CHASASAV>LGYYTPALTG-IWESYINLREWSSVLPCVAIFVGINHGSAKVDSDNNIQLSLTLAALSIDL

Parental  WWTFDRSRSGFGLGVGIAFLATLVTQLLVYNGVYQYTSPDFLYVRSWLPCIFFAGGITMGNIGR-QLAM
          .WTFD.S..GF.LGVGIA.LATLV.QLLVYNGVYQY.S.DFLYV.SWLPCIFFA.GITMGNIG..QLAM
Retrocopy GWTFDSSQNGFSLGVGIALLATLVAQLLVYNGVYQYRSSDFLYVHSWLPCIFFAAGITMGNIGN<QLAM

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_1872 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1872 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,