RetrogeneDB ID: retro_mdom_435

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:518870695..518871133(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010588
• Aliases: None
• Description: None

Sequence

>retro_mdom_435
AGTCACTACACCATGGGTGCCAAGGCTGTGGGGCCCCTCCATTAAGACTCCTCCATGACTGTCTTCTTCCCGGTCAGCAC
CAGTGAGTCCAAGCCCAGGCAGCTCAAGTTTCAAGTGATGTCCATGGACCCCAAGGATGTCCAAGGGCTGATGCAGCCCA
AGGTGAAGGTTCCCTTTTCTTCCAGTCATCTGAGTCCACCCCAGCCCTGAGGAACTTGTCCATAGCCCACCTCCTTGCCA
TCCCCTGAGTATGATCACCTGACTTGGTTAGGTATCTTAGTGTCCCAGAGTCTGCAGAAGACCTAGGGAAACTTCCTGGC
AGCTCTACTGATGGCTAGGGAAGTTTCTGGGCTCCAGAACTAAATTGAGTGAGAAAGAAACCAGATTCAAACCCTACAAC
AAGAGAAACAGAAGCTGTTTGATCAATTGATGGTGGCA

Alignment

ORF - retro_mdom_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.85 %
• Parental protein coverage: 66.06 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRYAMGVKAVGPLQYGSSMAALFRVGISEPEPGRPEFQVMFTDPKEAQGLMEPKAEVPFPPVRRRRTQPQ
          S.Y.MG.KAVGPL...SSM...F.V..SE..P....FQVM..DPK..QGLM.PK..VPF........QP.
Retrocopy SHYTMGAKAVGPLH*DSSMTVFFPVSTSESKPRQLKFQVMSMDPKDVQGLMQPKVKVPFSSSHLSPPQP*

Parental  PTCPEPAPLALPKRDPLTWFGILVPQSLRQAQGSFRAALLMAGEVAGLQSRIEWGRGQIQILLQEKRKLL
          .TCP.P..L..P..D.LTW.GILV.QSL....G.F.AALLMA.EV.GLQ..IE..R.QIQ.L.QEK.KL.
Retrocopy GTCP*PTSLPSPEYDHLTWLGILVSQSLQKT*GNFLAALLMAREVSGLQN*IE*ERNQIQTLQQEKQKLF

Parental  DQLKVA
          DQL.VA
Retrocopy DQLMVA

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_435 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_435 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010588	2 retrocopies	retro_mdom_200, retro_mdom_435 ,
Mus musculus	ENSMUSG00000042111	2 retrocopies	retro_mmus_2696, retro_mmus_380,
Oryctolagus cuniculus	ENSOCUG00000005099	1 retrocopy	retro_ocun_1651,
Otolemur garnettii	ENSOGAG00000000166	2 retrocopies	retro_ogar_2849, retro_ogar_3466,
Tursiops truncatus	ENSTTRG00000012598	1 retrocopy	retro_ttru_781,