RetrogeneDB ID: retro_mdom_480

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:715628127..715628373(+)
• Located in intron of: ENSMODG00000009815

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000023045
• Aliases: None
• Description: None

Sequence

>retro_mdom_480
TGTGAGAGGAGAGCTATATGACTGCAGGCAGTAATAGAGTCCGACATCCTCTGGTTCCACAGCACTGATGGTAAGAGAGA
AATCTGTCCCAGAGCCACTGCCACTGAACCGGGCAGGGACCCCAGGCTGCAGGCTGGAAGCCCCATAAATGAGGAGCCTG
GGAGACTGGCCTGGGGGATGTTGGTACCAGCTCATGTAATTACCAATGCTCTGACTGGCTCTGCAGGACAGGGAGACCGT
CTCTCC

Alignment

ORF - retro_mdom_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CERPGPSLLTVIVPDVFWFHTADGKRVICPRATATEPGRDARLQVGSIVNEEPGRLAWGLLVPVYAGTNA
          CER....L..VI..D..WFH..DGKR.ICPRATATEPGRD.RLQ.GS..NEEPGRLAWG.LVP....TNA
Retrocopy CERRAI*LQAVIESDILWFHSTDGKREICPRATATEPGRDPRLQAGSPINEEPGRLAWGMLVPAHVITNA

Parental  LTGPAGQGDRLS
          LTG.AGQGDRLS
Retrocopy LTGSAGQGDRLS

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_480 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_480 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 1 parental gene, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000023045	10 retrocopies	retro_mdom_471, retro_mdom_472, retro_mdom_474, retro_mdom_478, retro_mdom_480 , retro_mdom_482, retro_mdom_484, retro_mdom_486, retro_mdom_657, retro_mdom_658,