RetrogeneDB ID: retro_mdom_76

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:272970453..272970711(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024229
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000000970
• Aliases: None
• Description: None

Sequence

>retro_mdom_76
ATGGAGGAGTTGTGTCAGCCACCGCTTGAGGCCAAATCTGAAGTCACTAACAAGCTTCTAGATCTTCAGTGGAAAGTGAG
TATGGCAGTGAGCTCAGACAATTGCAGATCTCTTAAGTCTCCTTATGCTGCATTGATGCTAAAAGTGGCAGATCAGTCAG
GCCAGATAACAAACAAGTCCTTTGAAATGACAATTCCACAATTTCAGCATTTCTTCAAACAGTTTAAAGAAATGGCTGCT
GTTATTGAAACTGTGTAA

Alignment

ORF - retro_mdom_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEELCQPPLEAKSEVTNKLLDLQWKMGMAVSSDNCRSLKSPYVALMLKVADQSGQITNKSFEMTIPQFQH
          MEELCQPPLEAKSEVTNKLLDLQWK..MAVSSDNCRSLKSPY.ALMLKVADQSGQITNKSFEMTIPQFQH
Retrocopy MEELCQPPLEAKSEVTNKLLDLQWKVSMAVSSDNCRSLKSPYAALMLKVADQSGQITNKSFEMTIPQFQH

Parental  FFKQFKEMAAVIETV
          FFKQFKEMAAVIETV
Retrocopy FFKQFKEMAAVIETV

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_76 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_76 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011048	1 retrocopy	retro_dord_237,
Erinaceus europaeus	ENSEEUG00000006061	2 retrocopies	retro_eeur_120, retro_eeur_560,
Myotis lucifugus	ENSMLUG00000010697	1 retrocopy	retro_mluc_1927,
Monodelphis domestica	ENSMODG00000000970	3 retrocopies	retro_mdom_111, retro_mdom_147, retro_mdom_76 ,
Nomascus leucogenys	ENSNLEG00000026952	1 retrocopy	retro_nleu_2240,
Rattus norvegicus	ENSRNOG00000038012	1 retrocopy	retro_rnor_2012,
Tursiops truncatus	ENSTTRG00000003379	2 retrocopies	retro_ttru_1697, retro_ttru_908,