RetrogeneDB ID: retro_mdom_1548

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:200214994..200215247(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI1
• Ensembl ID: ENSMODG00000016577
• Aliases: None
• Description: desumoylating isopeptidase 1 [Source:HGNC Symbol;Acc:24577]

Sequence

>retro_mdom_1548
TTCCTGGAATAGCTGTTCTCCCTGGGTGTATCATTGTTCCAAGGTGATGCTTATAATTTCTTTGAGCACAACTGTAACAC
ATTCAGCAATGAAGTGGCCCAGTACCTGACTGGGAAGAAGATTCGCTCTTACATCACCCATCTTCCATCTGAAATCCTTT
CCATGCCTTTCAAACAGGATCAAAGGGTCTTCTGGATCTATCCAGATCCCACCTGGTGATGGGAACACCTTTGGCAGTTC
CAATGGCTATAGC

Alignment

ORF - retro_mdom_1548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 50.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLEYLSSLGESLFRGEAYNLFEHNCNTFSNEVAQFLTGKKIPSYITDLPSEVLSTPFGQALR-PLLD-SI
          FLE.L.SLG.SLF.G.AYN.FEHNCNTFSNEVAQ.LTGKKI.SYIT.LPSE.LS.PF.Q..R..LLD.SI
Retrocopy FLE*LFSLGVSLFQGDAYNFFEHNCNTFSNEVAQYLTGKKIRSYITHLPSEILSMPFKQDQR<GLLD<SI

Parental  QIQPPGGNTFGRPNGQS
          QI.P..GNTFG..NG.S
Retrocopy QIPPGDGNTFGSSNGYS

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_1548 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1548 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018941	1 retrocopy	retro_cjac_1874,
Echinops telfairi	ENSETEG00000005136	1 retrocopy	retro_etel_2107,
Monodelphis domestica	ENSMODG00000016577	2 retrocopies	retro_mdom_1548 , retro_mdom_684,
Ictidomys tridecemlineatus	ENSSTOG00000009480	1 retrocopy	retro_itri_1719,