RetrogeneDB ID: retro_mdom_108

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:375684116..375684914(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000029005
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000028443
• Aliases: None
• Description: None

Sequence

>retro_mdom_108
ATGCCATCTGTTTTCAGAGTACAAACAATCTTTTTCAGTCCTCCCTCTCTACAATACATACACACATACACACATGAGTT
CTATACCCTCTCTCTTCCCTCATCACCCCCACACCCCATCTTTAAATCCAAGTACTGCAAACCGAGACATCTTATATGCA
GAACTGCATTTGATGCTGGATCTATGCCTAGCAGATTGTTGCTGAGGGAAGAATCTGCCCTTTGCAAGATGTTGCCTGAG
GACCCTGTAAATTATTTGATTTTCCAAAAAGAAAAGAGAGAGGCACAGACAAAAAGTCAGACAGATATAAAGGAAGGAAG
GAAGCAAAAGAAAATGAAGGGAGAAAAGAAAGAGGCTAAAGAAATAAAAAGAGAATGCAAGAAGAAACATATACAGTTAT
ATGTAAAAAAGAGAGAAAAGGGAGGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA
GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGGAGGAAGAAA
GGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA
GGAAGGAAGGAAGGAAGGGAAGGAGGGAGAAAGGGAGGAAGGAAGGAAGGGGTTGTGGGAGAAACACACCCAAGTTTGAA
GCAGGGTCTCACCCCAAGAATGGGAGACTCAAACTGTGTTCAATCCAGAAGAAAAGAATTTTATTTGAAGAAGAAGTG

Alignment

ORF - retro_mdom_108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.24 %
• Parental protein coverage: 72.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KERKTERKREREREREKERKREREKERKREREKERKKERKKERKKERKKERKKERKKERKKERKKERKEG
          ...K.E............RK....K..K.E..KE.K.E.KK.......K.R.K..K..RK..RK..RKEG
Retrocopy QKEKREAQTKSQTDIKEGRKQKKMKGEKKEA-KEIKRECKKKHIQLYVKKREKGGKEGRKEGRKEGRKEG

Parental  RKEGRKEDRKTGRQEDRKTGGQKEKEEGRKEGGKEGGKEGRKEGRKEGRKEGRKEGRKEGRKGGREEGRN
          RKEGRKE.RK.GR.E.RK.G.......GRK.G.KEG.KEGRKEGRKEGRKEGRKEGRKEGRKG.RE.GR.
Retrocopy RKEGRKEGRKEGRKEGRKEGRKEGRKGGRKGGRKEGRKEGRKEGRKEGRKEGRKEGRKEGRKGRREKGRK

Parental  GGR
          .GR
Retrocopy EGR

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	0.20 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.50 RPM
SRP007412_testis	0.00 RPM	0.79 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_108 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_108 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000028443	1 retrocopy	retro_mdom_108 ,