RetrogeneDB ID: retro_mdom_225

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:246096555..246096804(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024593
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000028279
• Aliases: None
• Description: None

Sequence

>retro_mdom_225
ATGAGCTTCTTAAAATTTATGATGCAAAAGAAAGAACTTATTCCTTTAATCACATTTGTGAGTTTTGCAGGACTTGGAGC
TACCTACATGTCCGTATATTCCCTTTTCAAAACTGATGTGATTGTTAACAGGAAGAAAAATCCAGAACAATGGGAAAACG
TGAATCCTCATGAGGCTCAAAAGCTTTTAACAATTCACCAAAAGTGGGAACCTGTGGAAGAGTTGAGCACAGTCAAACAG
TTGACCAAA

Alignment

ORF - retro_mdom_225 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNFVQFLMKRKELIPLIAFVSMAGCGAVGISFYTLAKPDVILNRRQNPEPWENVNPNHPQKLITINQKWK
          M.F..F.M..KELIPLI.FVS.AG.GA...S.Y.L.K.DVI.NR..NPE.WENVNP...QKL.TI.QKW.
Retrocopy MSFLKFMMQKKELIPLITFVSFAGLGATYMSVYSLFKTDVIVNRKKNPEQWENVNPHEAQKLLTIHQKWE

Parental  PIEELQKVRKLTK
          P.EEL..V..LTK
Retrocopy PVEELSTVKQLTK

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	63.06 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_225 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_225 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031501	2 retrocopies	retro_cfam_1654, retro_cfam_669,
Cavia porcellus	ENSCPOG00000020706	1 retrocopy	retro_cpor_450,
Erinaceus europaeus	ENSEEUG00000003556	1 retrocopy	retro_eeur_594,
Monodelphis domestica	ENSMODG00000028279	1 retrocopy	retro_mdom_225 ,
Oryctolagus cuniculus	ENSOCUG00000029216	1 retrocopy	retro_ocun_33,
Rattus norvegicus	ENSRNOG00000050251	1 retrocopy	retro_rnor_484,
Sarcophilus harrisii	ENSSHAG00000006433	3 retrocopies	retro_shar_296, retro_shar_416, retro_shar_744,
Ictidomys tridecemlineatus	ENSSTOG00000021929	1 retrocopy	retro_itri_1133,