RetrogeneDB ID: retro_mdom_1775

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:56817594..56817822(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHURC1
• Ensembl ID: ENSMODG00000009664
• Aliases: None
• Description: churchill domain containing 1 [Source:HGNC Symbol;Acc:20099]

Sequence

>retro_mdom_1775
ATGCATGGGGACTTTGTGGAGAAGAAATATCCAAACCGGGGTAATACCTGCTTGGAGAATGGGTCTTTGTTGCTGAACTA
TGTAGACTGTGCAATGTTTAATAAATGAGATTTTATGTTGATTGCAAACAAATCCGTGAAAGAGGAAGATGGAGAAGAAA
TAGTTACATATGATCATGTATGTAAGAATTGTCATCACGTAGTAGCCAGAACTTTCAGTGTCATGGAT

Alignment

ORF - retro_mdom_1775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 70.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCGDCVEKEYPNRGNTCLENGSFLLNYVGCAMCNKRDFMLIANKSTKEEDGEEIVTYDHICKNCHHIVAR
          M.GD.VEK.YPNRGNTCLENGS.LLNYV.CAM.NK.DFMLIANKS.KEEDGEEIVTYDH.CKNCHH.VAR
Retrocopy MHGDFVEKKYPNRGNTCLENGSLLLNYVDCAMFNK*DFMLIANKSVKEEDGEEIVTYDHVCKNCHHVVAR

Parental  HEYTFSVMD
          ...TFSVMD
Retrocopy ---TFSVMD

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	48.04 RPM
SRP007412_cerebellum	0.00 RPM	56.48 RPM
SRP007412_heart	0.00 RPM	202.74 RPM
SRP007412_kidney	0.00 RPM	122.47 RPM
SRP007412_liver	0.00 RPM	68.47 RPM
SRP007412_testis	0.00 RPM	48.72 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1775 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1775 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
Myotis lucifugus	ENSMLUG00000004300	1 retrocopy	retro_mluc_2068,
Monodelphis domestica	ENSMODG00000009664	1 retrocopy	retro_mdom_1775 ,
Mustela putorius furo	ENSMPUG00000006792	1 retrocopy	retro_mputfur_554,
Oryctolagus cuniculus	ENSOCUG00000001838	1 retrocopy	retro_ocun_997,
Pteropus vampyrus	ENSPVAG00000011384	1 retrocopy	retro_pvam_406,