RetrogeneDB ID: retro_mdom_1118

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:147698444..147698905(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006055
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020366
• Aliases: None
• Description: None

Sequence

>retro_mdom_1118
TTTCTTGCCTTGTTCAGGCACACTCCTGTATCTCCCTTCGGGGGCAGATCAATATCCAGACGATTCTACCGAGGTGACAG
CCCAACAGACTCCCAAAAGGACATGCTTGATATCCCTTTGCCCCCATGGGAAGAGCGAACACATGAACCAATTGAAACCA
AGAGGGCCCGCCTGCTTTATGAGAGCAGGAAGAGAGGCATGCTAGAGAACTGCATCCTTCTGAACCTCTTTGCCAAGGAG
AATCTACACCAGATGACAGAGAGGCAGCTGAACCTCTATGACCGACTAATCAATGAGCCCAGTAATGACTGGGATATCTA
CTACTGGGCAACAGAAGCAAAGCTAGCCCCGAGATCTTTGAAAATGAAGTCATGGCAATGCTGAGGGACTTTGCCAAGAA
CAAGAATAAAGAACAGAGGCTGCGGGCCCCAGATCTCAAGTACCTCTTTGAGAAACCAACC

Alignment

ORF - retro_mdom_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLALFRHTLVSPFGGRSISRRFYQGDSPTDSQKDMLEIPLPPWEERTDEPIETKRARLLYESRKRGMLEN
          FLALFRHT.VSPFGGRSISRRFY.GDSPTDSQKDML.IPLPPWEERT.EPIETKRARLLYESRKRGMLEN
Retrocopy FLALFRHTPVSPFGGRSISRRFYRGDSPTDSQKDMLDIPLPPWEERTHEPIETKRARLLYESRKRGMLEN

Parental  CILLSLFAKENLHQMTERQLNLYDRLINEPSNDWDIYYWATEAKPA-PEIFENEVMAMLRDFAKNKNKEQ
          CILL.LFAKENLHQMTERQLNLYDRLINEPSNDWDIYYWATEAK.A.PEIFENEVMAMLRDFAKNKNKEQ
Retrocopy CILLNLFAKENLHQMTERQLNLYDRLINEPSNDWDIYYWATEAKLA<PEIFENEVMAMLRDFAKNKNKEQ

Parental  RLRAPDLEYLFEKPT
          RLRAPDL.YLFEKPT
Retrocopy RLRAPDLKYLFEKPT

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_1118 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1118 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005213	2 retrocopies	retro_chof_2032, retro_chof_2340,
Monodelphis domestica	ENSMODG00000020366	1 retrocopy	retro_mdom_1118 ,