RetrogeneDB ID: retro_mdom_1850

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:96301253..96301637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019863
• Aliases: None
• Description: None

Sequence

>retro_mdom_1850
CATGGAGAACTCCCTTACACGTATTCCAGAATTACAATGGAGTCAAATCCTCAATTATATCCTGTACTGGGCATGCTGAA
GAAGTGTACTGAAGAGAATACTGATCATACCTTCAACTCATTACTCTGCAATCTTTACTGAAACACAAAGGACAGAGTTG
ACTAACACAGCAATGATGAACTATCGCTGGGAAGATGCCACATCATCATTTCCCCTCAGGTTGGAGGCCACCTACATCTT
TGAAATGAGGAAGAAGCCTTCCCCATAAGAGAAAGGGTACCAAATACATATATATGGAAAAAGTAAAGATACCCTTGGAT
CATGAGACCTTGTTGATGATGGAGGAAGAGACTATAAGCTGACTGGCAGCACTAGGTGCCAAAG

Alignment

ORF - retro_mdom_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.77 %
• Parental protein coverage: 50.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YGELPYTYSRITMEPNPQWHPVLGTLKKRIEENSGHTFNSLLCNLYRNEKDSVDWHSDDEPALGRCPVIA
          .GELPYTYSRITME.NPQ..PVLG.LKK..EEN..HTFNSLLCNLY.N.KD.VD.HS.DE..LGRC..I.
Retrocopy HGELPYTYSRITMESNPQLYPVLGMLKKCTEENTDHTFNSLLCNLY*NTKDRVD*HSNDELSLGRCHIII

Parental  S-LSLGATRTFEMRKKP-PPEENGD-YTYMEKVKIPLDHGTLLMMEGATQ-ADWQHRVPK
          S.L.L.AT..FEMRKKP.P....G..Y.YMEKVKIPLDH.TLLMME..T..ADWQH.VPK
Retrocopy S>LRLEATYIFEMRKKP>PHKRKGTKYIYMEKVKIPLDHETLLMMEEETI>ADWQH*VPK

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_1850 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1850 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000019863	1 retrocopy	retro_mdom_1850 ,
Oryctolagus cuniculus	ENSOCUG00000016359	1 retrocopy	retro_ocun_1878,