RetrogeneDB ID: retro_mdom_441

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:541727159..541727919(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B1
• Ensembl ID: ENSMODG00000010776
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) [Source:HGNC Symbol;Acc:8574]

Sequence

>retro_mdom_441
GTGCAAGATATTTCCTTTGACTACAGTGGCAATATTTGGTTTCTTGTTCTACTGATATGTTCATCAAACTTACAGATTTC
CAGAATTCTGAGTCCATTATAACCATGCATAGCTATGATCACAATGACTTTTCAGTAGCCACCATGCCTAATGGAGATGA
TATATATCTTCCTCCAGGGACAAAACCATAAAAATGTGGGAAGTACAAAATGGCTACTGTTTAAAGTCTTCCACAGGCCA
CAGAGAATGGGTGTGTATGGTGTGCCCAAATAAGCATAGCACATCAATTTCTAGTTGTTCTTATGACCAGACAGTTTGTG
TATGGGTGGTTTCCACAAAGGAATTCAAAGTTGAGATCTGAGATCATGAGCATGTAGTCTAGTACACTTCATGGGCTTAT
TCCTCTATCTCTGAAGCTGCATAATTTGAGACTTAAAAAAAATCCAACAGGTAGCAAATCTGGACCAACTTCTTGTCTGG
ATCCAGAGACAAGACTATTAATATATGGGACATCATCATTGGCATATGCCTTATAACTCTTATGGGTCATGATAATTGGG
GACATGAACTTCTCTACCATTTGGGGGGAAAGCTTATTTTGAATTGTGATGATGACAAGACCCTACATGCATCTGACTAT
AAGAAGTAATGCATAAAGACCCTTCGGGTGCATAAACAGTTTGTAACCTCCTTAGATTTCTCTGAGACAGCACTATACAT
GATTACTGGAAGTATAGATTGAACAGTAAAAATGTGGAAG

Alignment

ORF - retro_mdom_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.22 %
• Parental protein coverage: 62.44 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VQDISFDHSGKL-LASCSADMTIKLWDFQGFECIRTMHGHDHNVSSVAIMPNGDHI-VSASRDKTIKMWE
          VQDISFD.SG...L.SCS.DM.IKL.DFQ..E.I.TMH..DHN..SVA.MPNGD.I..S.SRDKTIKMWE
Retrocopy VQDISFDYSGNI<LVSCSTDMFIKLTDFQNSESIITMHSYDHNDFSVATMPNGDDI<ISSSRDKTIKMWE

Parental  VQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSY
          VQ.GYC.K..TGHREWV.MV.PN...T.I.SCS.DQTV.VWVV.TKE.K.E...HEHVV...SWA....Y
Retrocopy VQNGYCLKSSTGHREWVCMVCPNKHSTSISSCSYDQTVCVWVVSTKEFKVEI*DHEHVV*YTSWA----Y

Parental  SSISEATGSETKKSSKPGPI---LLSGSRDKTIKMWDVITGMCLMTLVGHDNWVRGVLFHSGGKFILSCA
          SSISEA...ET...S....I....LSGSRDKTI..WD.I.G.CL.TL.GHDNW....L.H.GGK.IL.C.
Retrocopy SSISEAA*FETXXXSNR*QIWTNFLSGSRDKTINIWDIIIGICLITLMGHDNWGHELLYHLGGKLILNCD

Parental  DDKTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWE
          DDKTL...DYK.K.C.KTL..H..FVTSLDF..TA.Y..TGS.D.TVK.W.
Retrocopy DDKTLHASDYK-K*CIKTLRVHKQFVTSLDFSETALYMITGSID*TVKMWK

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_441 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_441 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000007168	2 retrocopies	retro_hsap_2144, retro_hsap_2292,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,
Monodelphis domestica	ENSMODG00000010776	2 retrocopies	retro_mdom_441 , retro_mdom_460,
Mus musculus	ENSMUSG00000020745	1 retrocopy	retro_mmus_2988,
Pongo abelii	ENSPPYG00000007796	1 retrocopy	retro_pabe_1932,
Pan troglodytes	ENSPTRG00000008551	1 retrocopy	retro_ptro_1569,
Sorex araneus	ENSSARG00000002826	4 retrocopies	retro_sara_266, retro_sara_275, retro_sara_364, retro_sara_588,