RetrogeneDB ID: retro_mdom_460

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:658510307..658510961(+)
• 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_460
CATGATCACAATGTCTCTTCAGTAGCCATCATACCTAATGAAAATCACATATTATCTGTCACCAGGGATAAAACTATAAA
AATCTGGGAAGTGCAAACTGGCTATTGTGTGGAGATTTTCACAAAACACAGAGAATGGGTACACATGGTGTGGCCAAGTC
AGGTGGGCACCTTAATTGCATGTTGTTTTAATAATCAGACAGTTCATATATAGGTAGTAGTGACAAAGGAATGCAAAGCT
GAGCTCAGAAAACACAAGCATGTGGTTGAGTGCATTTCCTGGGCCTCAGAAAGCTCTTATTCCTCTTTCTCTAAAGCTAC
AGGATCTGAGACTAAAAAAAGTAGCAAACCTGGATCTATCTTGCTGTCTGTATCCAGAGACAAGACCATTAACATGTGGT
ACATTATTGCTGGCATGTGCCTTATGACCCTTGTGGACCATGATAATTGGGCACATGGAGTTCTCTTCCATTCTAGGGGA
AAGTTTATTTTGAGTTGTGCTGTTGACAAGACCCTACATAGGTGGGACTATAAGAATAAACAATTGATGGAGACCCTCAA
CACCCATGAGCATTTTGTTACCTCCTTGGGTTTCTACAAGATGGCACCATACCTGGCTACTGGAAGTGTAGATCAAATAG
TAATAGTGAAGGAG

Alignment

ORF - retro_mdom_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.61 %
• Parental protein coverage: 53.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRV
          HDHNVSSVAI.PN..HI.S..RDKTIK.WEVQTGYCV..FT.HREWV.MV.P.Q.GTLIA.C.N.QTV..
Retrocopy HDHNVSSVAIIPNENHILSVTRDKTIKIWEVQTGYCVEIFTKHREWVHMVWPSQVGTLIACCFNNQTVHI

Parental  WVVATKECKAELREHEHVVECISWAPESSYSSISEATGSETKKSSKPGPILLSGSRDKTIKMWDVITGMC
          .VV.TKECKAELR.H.HVVECISWA.ESSYSS.S.ATGSETKKSSKPG.ILLS.SRDKTI.MW..I.GMC
Retrocopy *VVVTKECKAELRKHKHVVECISWASESSYSSFSKATGSETKKSSKPGSILLSVSRDKTINMWYIIAGMC

Parental  LMTLVGHDNWVRGVLFHSGGKFILSCADDKTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSV
          LMTLV.HDNW..GVLFHS.GKFILSCA.DKTL..WDYKNK..M.TLN.HEHFVTSL.F.K.APY..TGSV
Retrocopy LMTLVDHDNWAHGVLFHSRGKFILSCAVDKTLHRWDYKNKQLMETLNTHEHFVTSLGFYKMAPYLATGSV

Parental  DQTVKVWE
          DQ.V.V.E
Retrocopy DQIVIVKE

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_460 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_460 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,