RetrogeneDB ID: retro_mdom_1195

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:437915210..437916014(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000011300
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BSG
• Ensembl ID: ENSMODG00000006517
• Aliases: None
• Description: basigin (Ok blood group) [Source:HGNC Symbol;Acc:1116]

Sequence

>retro_mdom_1195
GTGGGGGCCCCGCTGCCGTGGCTGCTGGCAGCTGTGTTGCTCTGCGCTCGGGCGCCTCCGGAACTGGAAACGACATTTGG
ACAGCTATAGATGTTTCTAGCCATAGAACACTCCTGACCTGTAAATTGAAAGAAGCTCTTTCAGCTCCCACTGAGGGTCA
TGGATGGCTGAAGGGTGACAAGGTGTTGAAAGACGATAAATCGGAGAGTCTAACCACAGAATATGAGGTTGTGTCAGATG
ATAGATCCGGGGAGTATCAGTGCATTTTTCTTCCAGAACTTGCAGACTGATGTACAAGTAAAAGGTCCCCCGAAGGTTTA
TATGAACAAGAAGTCAGAATATGGGAATGAGGGAGACTCGATAGTTCTTACGTGTAAGAGTTCTTCCTATCCCTCTATTG
AACAATGGAAATGGTACAAAGACTATGAAGGGGAAGCTAATGTGATCCTTGTAAATGATACTGAAGGGAGGATGTCAATA
ATAAGCACCCCTGAAAAAACAGAGCTCCACATTAATTCAGCGGATATAAAGGAGGATCCTGGAAAGTACATCTGCAATGG
CACCAATTCTGAGGGCTCGGATACTGCTGTAATTACTTTGAAAGTGCGCAGCCGTCTGGCTGCACTTTGGCCCTTCCTGG
GCATTGTGGCAGAAGTTCTGATCCTTGTCATCATTATCTTCATCTATGAAAAGAGGAGCAGGACTGATGATATTCCTGAA
GATGAAGATGGAGGTGCCGCACCACTGAAATCCAGTTCGGCTGTGAATGAGAAAGGTAGCAACATTCGTCAGAGCAATTC
CAAC

Alignment

ORF - retro_mdom_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGAPLLWLLAAVLLCARA-ASGTGNNIWTAIDVSSHRTLLTCKLKEAISAPIEGHRWLKGDKVLKEDKSD
          .GAPL.WLLAAVLLCARA.ASGTGN.IWTAIDVSSHRTLLTCKLKEA.SAP.EGH.WLKGDKVLK.DKS.
Retrocopy VGAPLPWLLAAVLLCARA<ASGTGNDIWTAIDVSSHRTLLTCKLKEALSAPTEGHGWLKGDKVLKDDKSE

Parental  SLTTEYEVVSDDRS-GEYQCIFLPELAGKADVQVKGPPKVYINKKSEYGNEGDSIVLTCKSSSYPSIEQW
          SLTTEYEVVSDDRS.G.....F...L....DVQVKGPPKVY.NKKSEYGNEGDSIVLTCKSSSYPSIEQW
Retrocopy SLTTEYEVVSDDRS>GSISAFFFQNL--QTDVQVKGPPKVYMNKKSEYGNEGDSIVLTCKSSSYPSIEQW

Parental  KWYKENEGEANMILVNDTEGRMSIISTPEKTELHINSADIKEDPGKYICNGTNSEGSDTAVITLKVRSRL
          KWYK..EGEAN.ILVNDTEGRMSIISTPEKTELHINSADIKEDPGKYICNGTNSEGSDTAVITLKVRSRL
Retrocopy KWYKDYEGEANVILVNDTEGRMSIISTPEKTELHINSADIKEDPGKYICNGTNSEGSDTAVITLKVRSRL

Parental  AALWPFLGIVAEVLILVIIIFIYERRRRTDDIVEAEPPRDEDGGAAPLKASSAVNEKGSNIRQRNSN
          AALWPFLGIVAEVLILV.II......R...D......P.DEDGGAAPLK.SSAVNEKGSNIRQ.NSN
Retrocopy AALWPFLGIVAEVLILV-IIIFIYEKRSRTDDI----PEDEDGGAAPLKSSSAVNEKGSNIRQSNSN

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_1195 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1195 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019717	1 retrocopy	retro_cfam_1426,
Felis catus	ENSFCAG00000007837	1 retrocopy	retro_fcat_822,
Myotis lucifugus	ENSMLUG00000009184	1 retrocopy	retro_mluc_399,
Monodelphis domestica	ENSMODG00000006517	2 retrocopies	retro_mdom_1195 , retro_mdom_1203,
Mustela putorius furo	ENSMPUG00000009950	1 retrocopy	retro_mputfur_878,