RetrogeneDB ID: retro_mdom_1203

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:466513396..466513916(-)
• Located in intron of: ENSMODG00000015487

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1203
GATAGTTCAATCACAAAATATGAAGTTTTGTCAGATGAGAAATATGGGGAGTATCAGTGCATTTTTCTTGCCGAACTTGC
AGGAAAGGCTGATGTACAAGAAAAAGGTTTCCCAAAGATTGTTATTAAGAAAAAGGCAGAATATATGAGTGAGGGAGACT
CAGTAATCCTTATGTGTAAGAGTTATTCCTATCCCCCTGTTGAACACTGGACATGGTTCAAAGAATATGAGATGGAAGGT
AATGTGGCCCTTGTAAATGAAACTGTAAGGAGCAGCATAATAATAGATATTCCTGAAAACACAAAGCTGCAGATTAATTT
GGCAGATATAAAGAAAGATCCTGGAAAATACACTTACAATAGCACCAACTCTGAGGGCTCTGGTGCTGTTGTAATCACTT
TGAAGGTGATCAGCCATCTGGCTGCACTCTGGCTCTTCCTGGGCATTGCAGCAGAGGTTGTTGGTCTTTGTCATCATTGT
TTTGGTCTATGAAAAGAGAAGGTCTGAAGATTTTGTTGAA

Alignment

ORF - retro_mdom_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.43 %
• Parental protein coverage: 63.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSLTTEYEVVSDDRSGEYQCIFLPELAGKADVQVKGPPKVYINKKSEYGNEGDSIVLTCKSSSYPSIEQW
          DS..T.YEV.SD...GEYQCIFL.ELAGKADVQ.KG.PK..I.KK.EY..EGDS..L.CKS.SYP..E.W
Retrocopy DSSITKYEVLSDEKYGEYQCIFLAELAGKADVQEKGFPKIVIKKKAEYMSEGDSVILMCKSYSYPPVEHW

Parental  KWYKENEGEANMILVNDTEGRMSIISTPEKTELHINSADIKEDPGKYICNGTNSEGSDTAVITLKVRSRL
          .W.KE.E.E.N..LVN.T.....II..PE.T.L.IN.ADIK.DPGKY..N.TNSEGS...VITLKV.S.L
Retrocopy TWFKEYEMEGNVALVNETVRSSIIIDIPENTKLQINLADIKKDPGKYTYNSTNSEGSGAVVITLKVISHL

Parental  AALWPFLGIVAEV-LILVIIIFIYERRRRTDDIVE
          AALW.FLGI.AEV.L..VII...YE..RR..D.VE
Retrocopy AALWLFLGIAAEV>LVFVIIVLVYE-KRRSEDFVE

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_1203 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1203 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,