RetrogeneDB ID: retro_mdom_718

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:208840908..208841817(+)
• Located in intron of: ENSMODG00000028071

Retrocopy information

• Ensembl ID: ENSMODG00000010288
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IRAK4
• Ensembl ID: ENSMODG00000018536
• Aliases: None
• Description: interleukin-1 receptor-associated kinase 4 [Source:HGNC Symbol;Acc:17967]

Sequence

>retro_mdom_718
TTAGAAGTTAGTGATACACATTTCCAGAGTTTTTCATTTCATGAGTTAAAGAGTGTTATAAATAATTTTGATGAGCGCGC
TATGTCCGCTGGTGGAAACAAAATGGGAAAGGGAGACTTTGGAGTTGTACAAAAAGGCTATATCAATAGCAGAACCATGG
CAGTGAAGAAACTTACAATGATGGCTGTTATGTGTACTGAAGAACTAAAACAATTTGATCAGGAAATAAAAATACTGACA
AAGTGTCAACATGAAAACTTAGTACAACTGTTTGGTTTCTCAAGTGACAGCGATGACTTCTGTTTGGTGTATGTCTATAT
GCCCAGTGATTCATTGCTTGACAGAGTATCTTGTCTGGATGGTACTGAACCACTTTCCTATCATACAAGATGCAAAATTG
CTCAAGGTACAGCTAATGGTATCTACTACTTACCTGCAAACAATCATGTTCATAGAAATATTAAAAGTGCAAATATTTTA
CCTGATGAGGGCTTCTTATCCAAGATTTCTTACTTTAGACTTGGCACTAACTTCTACAAAATTTAACCAAATAGTCATGA
CTAGCAGAATTATAGTGACAACAGCCTATATGGCACCTAAAGCTTTGAGAGGAGAGATAATATCTAAATCTGACATTTAT
AGTTTTGGTGTGGTCTTGCTTGGAAATAATAACCAAACTTCCAGCAGCAGATGAACAGCATGAACCTCAATTACTGCTAG
ATATCAAAGAAGATATTGAAGATGAAGAAAAGCCAAGCTGAAGATTATATTGATGCAAAAATGAATGATGTCAATTCCAC
TTCTGTTGAAAATATGTATTCTATTGCTAATCTTTGTCTTCATGAAAAGGAAAATAAGAGACCAGACATTGAGGTGGTAA
AACGTCACCTCCAAAAGATGACGTCTTCC

Alignment

ORF - retro_mdom_718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 66.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LEVSDTRFQSFSFYELKSVTNNFDERPMSAGGNKMGEGGFGVVYKGCINSRTVAVKKLTRMTDMCTEELK
          LEVSDT.FQSFSF.ELKSV.NNFDER.MSAGGNKMG.G.FGVV.KG.INSRT.AVKKLT.M..MCTEELK
Retrocopy LEVSDTHFQSFSFHELKSVINNFDERAMSAGGNKMGKGDFGVVQKGYINSRTMAVKKLTMMAVMCTEELK

Parental  QQFDQEIKILAKCQHENLVQLLGFSSDSNDFCLVYVYMPNGSLLDRLSCLDGTEPLSWQTRCKIAQGTAN
          Q.FDQEIKIL.KCQHENLVQL.GFSSDS.DFCLVYVYMP..SLLDR.SCLDGTEPLS..TRCKIAQGTAN
Retrocopy Q-FDQEIKILTKCQHENLVQLFGFSSDSDDFCLVYVYMPSDSLLDRVSCLDGTEPLSYHTRCKIAQGTAN

Parental  GIYYLHANNHVHRDIKSANILLDEDFLPKISDF-GLARTSAKFNQTVMTSRIVGTTAYMAPEALRGEITP
          GIYYL.ANNHVHR.IKSANIL.DE.FL.KIS.F..LA.TS.KFNQ.VMTSRI..TTAYMAP.ALRGEI..
Retrocopy GIYYLPANNHVHRNIKSANILPDEGFLSKISYF>DLALTSTKFNQIVMTSRIIVTTAYMAPKALRGEIIS

Parental  KSDIYSFGVVL-LEIITGLPAVDEQREPQLLLDIKEEIEDEEK-HIEDYIDAKMNDVDSTSVENMYSIAT
          KSDIYSFGVVL.LEIIT.LPA.DEQ.EPQLLLDIKE.IEDEEK...EDYIDAKMNDV.STSVENMYSIA.
Retrocopy KSDIYSFGVVL>LEIITKLPAADEQHEPQLLLDIKEDIEDEEK>QAEDYIDAKMNDVNSTSVENMYSIAN

Parental  LCLHEKKNKRPDTEMVKHHLQKMTSS
          LCLHEK.NKRPD.E.VK.HLQKMTSS
Retrocopy LCLHEKENKRPDIEVVKRHLQKMTSS

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_718 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_718 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
Choloepus hoffmanni	ENSCHOG00000005497	1 retrocopy	retro_chof_1982,
Monodelphis domestica	ENSMODG00000018536	1 retrocopy	retro_mdom_718 ,