RetrogeneDB ID: retro_mdom_1844

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:68928297..68928609(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM1
• Ensembl ID: ENSMODG00000007076
• Aliases: None
• Description: LYR motif containing 1 [Source:HGNC Symbol;Acc:25074]

Sequence

>retro_mdom_1844
ACTACAACAATATGACAAGAATTTCTCAGCCTGTACTGCAGAATTTTCAGGTTTTCATGGGGGTGACATGCAGCTTCGGG
ACAGATAGAACACACCATCAAAGAAAATCAGTATGATCCAAATGAATCTAAAATGTTCCAGAAAAACAGAAGCTTTACTG
ATTCAGAATTTATTAAACAATGCATAGAGGAATACCTAGCAAGAATTGAAGTGGGATTGCATTATCAGATCCCATATCCA
AGGTCAATTCATCTGCCTCCGCTAGCCCTCACTCCCCTATAAAATCATGGACTTAAAACCCAGGAAAAGATC

Alignment

ORF - retro_mdom_1844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 86.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTATRQEVLGLYRKIFRLARRWHAASGQMEDTIREKQYIINEARILFQKNKNLTDSELIKQCIDECTARI
          TT...QE.L.LY..IFR.....HAASGQ.E.TI.E.QY..NE....FQKN...TDSE.IKQCI.E..ARI
Retrocopy TTTI*QEFLSLYCRIFRFSWG*HAASGQIEHTIKENQYDPNESK-MFQKNRSFTDSEFIKQCIEEYLARI

Parental  EIGLHYQIPYPRPIHLPPTALSPLQSRGFQNQEKL
          E.GLHYQIPYPR.IHLPP.AL.PL...G...QEK.
Retrocopy EVGLHYQIPYPRSIHLPPLALTPL*NHGLKTQEKI

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_1844 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1844 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 3 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008951	1 retrocopy	retro_cpor_873,
Monodelphis domestica	ENSMODG00000007076	3 retrocopies	retro_mdom_1844 , retro_mdom_721, retro_mdom_807,
Sarcophilus harrisii	ENSSHAG00000006127	6 retrocopies	retro_shar_156, retro_shar_270, retro_shar_709, retro_shar_795, retro_shar_798, retro_shar_801,