RetrogeneDB ID: retro_mdom_1288

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:295969136..295969334(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A1
• Ensembl ID: ENSMODG00000025577
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) [Source:HGNC Symbol;Acc:2287]

Sequence

>retro_mdom_1288
CAATCCTTCAGCTCCAGTACCAGAAACCATTTTGTGAATAAAGTAGCTGAAAAACTAAAACTCTTCCAGGAAAACAATGA
CCTCCCAGTCCACCTGCAGGGTAAGGGCCAAGACAATCTCCTATACAAATGAACAATAGCAATGTGCTTGGAAGGCACTT
CCTACAGTCTCTTCTGCCTTGGCTGGGCTTCCTTCCCC

Alignment

ORF - retro_mdom_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 92.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSFSSSSRNFFENRVAEKQKLFQENNDLPVYLKGGTGDQLLFTITMTMSVVGTGYCLFFLTWASFP
          .SFSSS.RN.F.N.VAEK.KLFQENNDLPV.L.G...D.LL...T..M...GT.Y.LF.L.WASFP
Retrocopy QSFSSSTRNHFVNKVAEKLKLFQENNDLPVHLQGKGQDNLLYK*TIAMCLEGTSYSLFCLGWASFP

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_1288 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1288 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012840	1 retrocopy	retro_chof_305,
Echinops telfairi	ENSETEG00000007654	1 retrocopy	retro_etel_2078,
Myotis lucifugus	ENSMLUG00000012331	1 retrocopy	retro_mluc_187,
Macaca mulatta	ENSMMUG00000000250	3 retrocopies	retro_mmul_1665, retro_mmul_1968, retro_mmul_2489,
Monodelphis domestica	ENSMODG00000025577	1 retrocopy	retro_mdom_1288 ,
Pan troglodytes	ENSPTRG00000010888	1 retrocopy	retro_ptro_125,