RetrogeneDB ID: retro_mdom_399

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:405236160..405236497(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002025
• Aliases: None
• Description: None

Sequence

>retro_mdom_399
ATGGCGGAGAAATTTGACCATCTGGAAGAACATCTGGAGAAATTCGTGAAGAACATCCATCAGCTTGGCATCATTATCAG
CGACTTCCAGCCCAGCAGCCAGGTGGGGCTCAACCAGAAACTGAATGTTATTGTGACTGGCTTACAGGATATTGAAAAAT
GTCTATAACAGCTTCATGATATTAGTGTTCCTTTAGAAGTTTTTGAATATATTGATCAAGGCCGTAATCCCCAAGCTGTA
CACCAAAGAGTGCCTGGAGAGGGCTCTAGCCAAAAATGAACAAGTTAAAAGCAAAATTGACACTATGAAGAAATTTAAAA
GCCTGTTGATTCAAGAT

Alignment

ORF - retro_mdom_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEKFDHLEEHLEKFVENIRQLGIIVSDFQPSSQAGLNQKLNFIVTGLQDIDKCRQQLHDISVPLEVFEY
          MAEKFDHLEEHLEKFV.NI.QLGII.SDFQPSSQ.GLNQKLN.IVTGLQDI.KC..QLHDISVPLEVFEY
Retrocopy MAEKFDHLEEHLEKFVKNIHQLGIIISDFQPSSQVGLNQKLNVIVTGLQDIEKCL*QLHDISVPLEVFEY

Parental  IDQGRNPQ-LYTKECLERALAKNEQVKGKIDTMKKFKSLLIQE
          IDQGRNPQ.LYTKECLERALAKNEQVK.KIDTMKKFKSLLIQ.
Retrocopy IDQGRNPQ>LYTKECLERALAKNEQVKSKIDTMKKFKSLLIQD

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_399 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_399 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006767	1 retrocopy	retro_amel_1034,
Canis familiaris	ENSCAFG00000010346	1 retrocopy	retro_cfam_721,
Dasypus novemcinctus	ENSDNOG00000004579	1 retrocopy	retro_dnov_1286,
Equus caballus	ENSECAG00000023738	1 retrocopy	retro_ecab_796,
Echinops telfairi	ENSETEG00000000027	1 retrocopy	retro_etel_1758,
Monodelphis domestica	ENSMODG00000002025	1 retrocopy	retro_mdom_399 ,
Otolemur garnettii	ENSOGAG00000005988	1 retrocopy	retro_ogar_1830,
Ochotona princeps	ENSOPRG00000015506	1 retrocopy	retro_opri_834,
Tupaia belangeri	ENSTBEG00000014579	2 retrocopies	retro_tbel_1647, retro_tbel_4561,
Tarsius syrichta	ENSTSYG00000002763	1 retrocopy	retro_tsyr_792,