RetrogeneDB ID: retro_mdom_684

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:93307745..93308126(+)
• 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_684
CTTGCCCTTGATAAGTCCATCGCATAAGTCTGGCACACCCCCATCATGATTTACAAGGATGAATTCTTCTTCAGCAGTGG
CAGAGCTTCCAGCTGTCCTCCTTGAGAGACACTGCTTGGGCCCACAGACTCTATTATTGCAGTGGGAAGCACTGAATGAT
TGAAGAAATCTTCTTGCAATACCTGTCCTCCTTAGGGGAGTCCCTGTTCTGATCGGAGATCTAGAATCTATTTATGTACA
ACTATAATTCTTTCAGCAAAGAAGTGACCCAGTTTTTAACAGGGAAACCTATTTCCCTCCTACATTACAAACCTTCCATC
TGAAGAACTCTCTATACCCTTTGGGAAGGGTTGGTGTCCCATCTCTGACTTTATCACTTTA

Alignment

ORF - retro_mdom_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.24 %
• Parental protein coverage: 75.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IMLGKQLEGIWHTSIVVHKDEFFFGSGGISSCPPGGTLLGPPDTVVEVGSTE-VTEEIFLEYLSSLGESL
          ..L.K.....WHT.I...KDEFFF.SG..SSCPP..TLLGP.D....VGSTE...EEIFL.YLSSLGESL
Retrocopy LALDKSIA*VWHTPIMIYKDEFFFSSGRASSCPP*ETLLGPTDSIIAVGSTE<MIEEIFLQYLSSLGESL

Parental  FRGEAYNLFEHNCNTFSNEVAQFLTGKKI-PSYITDLPSEVLSTPFGQALRPLLDSIQI
          F..E..NLF..N.N.FS.EV.QFLTGK.I.PSYIT.LPSE.LS.PFG....P..D.I..
Retrocopy F*SEI*NLFMYNYNSFSKEVTQFLTGKPI>PSYITNLPSEELSIPFGKGWCPISDFITL

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_684 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_684 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,