RetrogeneDB ID: retro_mdom_1100

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:108942478..108943007(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025104
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAKD
• Ensembl ID: ENSMODG00000011245
• Aliases: None
• Description: dephospho-CoA kinase domain containing [Source:HGNC Symbol;Acc:26238]

Sequence

>retro_mdom_1100
CTAGTCTTTCTAAAACAGGATATTTCTAGTGGATCTCAGGAAAGAGTTCATGTGTTCAGGGATCAGGGCTATGCTGTAAT
TAGTGAAATGCCATTGTCTACCAGGCAGTGAAGCTAAACTATCCTGCCTATCATATTGTGCAAGTCTTTGGACAAGAGAT
CCTGCTAGAGAATGATGAGATAAATCACCAGACTTCAGGAAGCTTACTCTTTCATCAGTCTGAGAAGCATAACCTGTTGA
TTGTCATCACCCATCCAGACATCTGTAAAGAGATGTTGAAGCAGGTCCTGAAGAACTTAGTTCAAGGGTACCAATATGTG
GTCTTGGAACTCCCTTTGGTGTTTGAAACCAAAACAATGTTATGATTCATGAAGCATGCAGTGGTGGTATATTCTGAAGC
CCAGAAGCAACTGTCATGGTTAATAGAACATAATGGGATGAGTTGAGAGGAGACTGAGGCACAGATTCAGCCCTTCTGTC
CCTGGAAGAGAAGCTCCAACCAACTCAGCACATCCTGAACAACTTGGGA

Alignment

ORF - retro_mdom_1100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.22 %
• Parental protein coverage: 78.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVGLSGGIASGKSSVIQVFRDLGCAVIDA-DDIAHQVVKPGFPAYYRIVQAFGHEILLENGEINRQALGS
          LV.L...I.SG......VFRD.G.AVI.....I..Q.VK...PAY..IVQ.FG.EILLEN.EIN.Q..GS
Retrocopy LVFLKQDISSGSQERVHVFRDQGYAVISE<NAIVYQAVKLNYPAYH-IVQVFGQEILLENDEINHQTSGS

Parental  IIFHQSEKRKLLNAITHPDIRKEMLKQVLKYLIQGYRYVILDIPLLFETKTMLRFMKHTVVVYCDPQTQL
          ..FHQSEK..LL..ITHPDI.KEMLKQVLK.L.QGY.YV.L..PL.FETKTML.FMKH.VVVY...Q.QL
Retrocopy LLFHQSEKHNLLIVITHPDICKEMLKQVLKNLVQGYQYVVLELPLVFETKTML*FMKHAVVVYSEAQKQL

Parental  SRLMERNGLSQEEAEARI-AAQLPLEEKRQLAQHILDNSG
          S.L.E.NG.S.EE.EA.I..A.L.LEEK.Q..QHIL.N.G
Retrocopy SWLIEHNGMS*EETEAQI<SALLSLEEKLQPTQHILNNLG

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_1100 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1100 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032388	1 retrocopy	retro_cfam_990,
Monodelphis domestica	ENSMODG00000011245	1 retrocopy	retro_mdom_1100 ,
Mus musculus	ENSMUSG00000020935	1 retrocopy	retro_mmus_1588,