RetrogeneDB ID: retro_mdom_246

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:31292410..31293022(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000017377
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016803
• Aliases: None
• Description: None

Sequence

>retro_mdom_246
CCCGGTTCTGGCCCGGGCCCTGGCGGTAGCGGTGAGAAAGGCCCCGTCGAGTCGGCACCAGGCCCGCCCGAGGAAGTCGT
AGTGTGGAGTCCCGAGGTGGAAGTGTGCCTCTTCCATGCCATGCTGGGGCACAAGCCTGTCGGTGTGAATCGGCACTTCC
ACATGATCTGCATCAGGGACAAGTTCAGTCAGAACATAGGGAGGCAGATCTCCTCCAAAGTCATCTGGGACCATTTAAGT
ACTATGTACGATATGCAAGCATTGCATGAGTCTGAGATTCTTCCATTCCCTAATTCAGAGAAGAACTTCATCCTTCCTGA
AGAAATTATTCAAGAGGTCAAAGAAGGAAAGGTGATGATTGAAGATGAGGTGAAGGAAGAAATAAAAGAAGAAATGGATT
CACACACTGGTACTGAAGATGTTTTTACCTCTTCAGGAAATTTGGGTAAAGGAGCTGAAAAGTCCAGTGGCAAAGAAAAA
GAAAAGAGCTCATCAGATTCTGGGTCTAAAGAAGGTGCAGACAAGAGGAAACGCAACCGTGTCACGGAAAAGGTCTTAAA
TGCAAACAGCAACCCCTCTAGCCCAAGTGCAGCCAAACGTCGGAGAACATAG

Alignment

ORF - retro_mdom_246 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  PGSGPGPGGSGEKGPVESAPGPPEEVVVWSPEVEVCLFHAMLGHKPVGVNRHFHMICIRDKFSQNIGRQI
          PGSGPGPGGSGEKGPVESAPGPPEEVVVWSPEVEVCLFHAMLGHKPVGVNRHFHMICIRDKFSQNIGRQI
Retrocopy PGSGPGPGGSGEKGPVESAPGPPEEVVVWSPEVEVCLFHAMLGHKPVGVNRHFHMICIRDKFSQNIGRQI

Parental  SSKVIWDHLSTMYDMQALHESEILPFPNSEKNFILPEEIIQEVKEGKVMIEDEVKEEIKEEMDSHTGTED
          SSKVIWDHLSTMYDMQALHESEILPFPNSEKNFILPEEIIQEVKEGKVMIEDEVKEEIKEEMDSHTGTED
Retrocopy SSKVIWDHLSTMYDMQALHESEILPFPNSEKNFILPEEIIQEVKEGKVMIEDEVKEEIKEEMDSHTGTED

Parental  VFTSSGNLGKGAEKSSGKEKEKSSSDSGSKEGADKRKRNRVTEKVLNANSNPSSPSAAKRRRT
          VFTSSGNLGKGAEKSSGKEKEKSSSDSGSKEGADKRKRNRVTEKVLNANSNPSSPSAAKRRRT
Retrocopy VFTSSGNLGKGAEKSSGKEKEKSSSDSGSKEGADKRKRNRVTEKVLNANSNPSSPSAAKRRRT

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	44.22 RPM
SRP007412_cerebellum	0.00 RPM	36.24 RPM
SRP007412_heart	0.00 RPM	15.55 RPM
SRP007412_kidney	0.00 RPM	11.85 RPM
SRP007412_liver	0.00 RPM	9.57 RPM
SRP007412_testis	0.00 RPM	7.66 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_246 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_246 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000020272	1 retrocopy	retro_cpor_1438,
Monodelphis domestica	ENSMODG00000016803	1 retrocopy	retro_mdom_246 ,
Mus musculus	ENSMUSG00000027569	1 retrocopy	retro_mmus_1383,
Sarcophilus harrisii	ENSSHAG00000010685	1 retrocopy	retro_shar_128,
Ictidomys tridecemlineatus	ENSSTOG00000012953	1 retrocopy	retro_itri_634,