RetrogeneDB ID: retro_mdom_1365

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:157542383..157542841(-)
• Located in intron of: ENSMODG00000004227

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADA
• Ensembl ID: ENSMODG00000016207
• Aliases: None
• Description: adenosine deaminase [Source:HGNC Symbol;Acc:186]

Sequence

>retro_mdom_1365
ATTAAAGTCAGGTCTATTCTATACTGCATGCACCATATACCAAATTGGTCCCCTAAGGTGGTGGAATTGTGTAAGAAGTA
TAGCCACCAGACTATGGTGGCCATCGACCTGTCTGGAAATGAGACCATTAAGGATAGTAGCCTCTTTCCTGGGCATTACA
GGCCTATGAGGAAGCTGTGAAAAATGGGATTCATCGGACAGTTCTTGCTGGAGAAGTGGGGCCACCCAAGGTTGTCCAGC
AAGCATTGGATGTTCTCCATGCTGAGAGGATAGACCATGGCTACCACACTCTGGAAGACCCTATCCTGTATAACAAATTG
CTGAAGGAGGACATGCATTTTGAGGTATGTCCCTGGTCGAGCTATCTCACAGGAGCCTGGAAACCAGACACACAGCATGC
GGTAGAAGGATTTAAAGAAAATAAGGCTAACTATTCACTCAACACCGATGACCCCCTC

Alignment

ORF - retro_mdom_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.36 %
• Parental protein coverage: 51.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKVRSILCCMRHMPNWSPEVVELCKKYRHQTVVAIDLAGDETIEDSSLFTGH-VQAYEEAVKSGIHRTVH
          IKVRSIL.CM.H.PNWSP.VVELCKKY.HQT.VAIDL.G.ETI.DSSLF.GH..QAYEEAVK.GIHRTV.
Retrocopy IKVRSILYCMHHIPNWSPKVVELCKKYSHQTMVAIDLSGNETIKDSSLFPGH<LQAYEEAVKNGIHRTVL

Parental  AGEVGPPKVVQQAVDVLHAERIGHGYHTLEDPTLYNKLLKEDMHFEVCPWSSYLTGAWKPDTQHAVIRFK
          AGEVGPPKVVQQA.DVLHAERI.HGYHTLEDP.LYNKLLKEDMHFEVCPWSSYLTGAWKPDTQHAV..FK
Retrocopy AGEVGPPKVVQQALDVLHAERIDHGYHTLEDPILYNKLLKEDMHFEVCPWSSYLTGAWKPDTQHAVEGFK

Parental  DDKANYSLNTDDPL
          ..KANYSLNTDDPL
Retrocopy ENKANYSLNTDDPL

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	23.60 RPM
SRP007412_cerebellum	0.00 RPM	13.38 RPM
SRP007412_heart	0.00 RPM	18.54 RPM
SRP007412_kidney	0.00 RPM	11.85 RPM
SRP007412_liver	0.00 RPM	45.31 RPM
SRP007412_testis	0.00 RPM	2.75 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1365 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1365 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	ENSCAFG00000009498	1 retrocopy	retro_cfam_744,
Macaca mulatta	ENSMMUG00000010603	1 retrocopy	retro_mmul_382,
Monodelphis domestica	ENSMODG00000016207	1 retrocopy	retro_mdom_1365 ,