RetrogeneDB ID: retro_mdom_1408

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:336778823..336779399(-)
• Located in intron of: ENSMODG00000005198

Retrocopy information

• Ensembl ID: ENSMODG00000005205
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLIC3
• Ensembl ID: ENSMODG00000017298
• Aliases: None
• Description: chloride intracellular channel 3 [Source:HGNC Symbol;Acc:2064]

Sequence

>retro_mdom_1408
CCCAGACTCCAGCTGTTTGTCAAGGCCAGTGAAGATGGTGAGAGTGTAGGGAGCTGTCTCTTCTGCCATCTTCTCTTCAT
GATCGCTACTACTCAAAGAATTTCCCTTCAATCTTTCCTCTGTGGACACCAAGAGGTCCTTGGAAGTGCTGAAGGACTTT
CTCCCTGCTCCCAGTGGCCCATACTGCTGTATGATAGGGAAGACGAGGTAGATACCGTCCAGATTGAAGAGTTCTTGGAA
GAGACACTGGAGCCATCCAACTTCCCCAGCCTGGTTCCTCCATGTAAGGGTCTAAGAACTGGTGGTGATGTCTTCCATAA
GTTCTCAGATTTCATCAAATACAGTTCTCTTGCTCAGGATGAAAGCTTATATGAGCCCTTGCTTCATGCTCTGGTGAAAT
CCAATCAATATCTGAACATAACCCCAGAGCCTGAGCTGAGTTGGTACCCCAAGATCACTCAGACCTGGCCTTGCTTCTTA
GCTGGCAACCAACTCATCTTGGCCAGTTACAACCTTCTACCTAAGCACATGGGCAGTACTGTGTGTACCTCCTGATGGTA
GACCCCCATCCCTGCC

Alignment

ORF - retro_mdom_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.76 %
• Parental protein coverage: 77.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKLQLFVKASEDGESVGNCPFCQRLFMI-LLLKGVPFTLTTVDTKRSLDVLKDFAPG-SQLPILLYDGEA
          P.LQLFVKASEDGESVG.C.FC..LFMI.LLLK..PF.L..VDTKRSL.VLKDF.P..SQ.PILLYD.E.
Retrocopy PRLQLFVKASEDGESVGSCLFCHLLFMI>LLLKEFPFNLSSVDTKRSLEVLKDFLPA<SQWPILLYDRED

Parental  KTDNIQIEEFLEEILGPPKYPSLVPRYKESNMAGNDVFHKFSAFIKNTSPSQDEAFYRPLLRALVKLDHY
          ..D..QIEEFLEE.L.P...PSLVP..K.....G.DVFHKFS.FIK..S..QDE..Y.PLL.ALVK...Y
Retrocopy EVDTVQIEEFLEETLEPSNFPSLVPPCK-GLRTGGDVFHKFSDFIKYSSLAQDESLYEPLLHALVKSNQY

Parental  LNTPLEHELIRDPKLTQSRRHFLDGDQLTLADCNLLPKLHIINTVCTYYRQAPIPA
          LN...E.EL...PK.TQ....FL.G.QL.LA..NLLPK.H...TVCT.....PIPA
Retrocopy LNITPEPELSWYPKITQTWPCFLAGNQLILASYNLLPK-HMGSTVCTS*W*TPIPA

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	3.81 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	4.59 RPM
SRP007412_kidney	0.00 RPM	18.44 RPM
SRP007412_liver	0.00 RPM	3.02 RPM
SRP007412_testis	0.00 RPM	19.64 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1408 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1408 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166,
Monodelphis domestica	ENSMODG00000017298	1 retrocopy	retro_mdom_1408 ,