RetrogeneDB ID: retro_sara_364

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_180116:902..1759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B1
• Ensembl ID: ENSSARG00000002826
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) [Source:HGNC Symbol;Acc:8574]

Sequence

>retro_sara_364
ACTAGAGTGATTTTCCATCCCATATTTACTATTATCATTTTGTTCTCAGAAGATGCTACAATTAATACCTGGGAATATGA
AACTGGAGCTTTGGAACAAACATTGAAAGACCAAAAGACTCATATCAGGATACTTAATTTGACCAGAGGGGGAAATCGCT
CGCCTGCTGCTTCACAGATACAACCATAAGACTGTGAGAATTTCAAAAGTCTCTCGCACTAGAACTATCTATGGCTATGA
ACACAATACTTCTTCAGTTGCCATCATGTCCAATAGAGATTTTACCATATCAGCCTTACGGGTTACAACCTTATAGATGT
GGGATAAACACACAGGCTGCTGTGTGAAGGCATTCACTAGCTACACAAAGTGGGTATGTATGGTGCCCCCAAACCAGGAT
GGCAAGCTGATAGCAAGCTGTTCTCATGAGCACACTATGACTGTTTGGAATACAGCCACTATATACTGTAAGAGCCGATG
TTGTGAACATAAGTATGTAGTAGAATGTATTTCCTGGATTCTTGAAGGTTCACATCCTTCCGTTGTGCAAGCAATGTGTA
CTGATACTGAACAATGGAGCAAGCCTGGAATTAATTTACTCTATGGATATAGAGATAAGATGATTAAGATGTGGGTCATT
ACCACTGACAAGAGCCTTATGTCCCCAGTGGGTCACAATGACTGGGTGTGTGGGGTCCTAGTGCATCCTCTAGGGACCTT
TATCATGAGCTGTGCAGATGACAAGAACTTATGTCTATGAACTTATAAGAATGGAGGATGCATCAAGACTATCAATGTGC
ATAATCATTCTGTAGTCCACCTTGAATGTCCATAAGATGACCCACTATGTGGTGACT

Alignment

ORF - retro_sara_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.29 %
• Parental protein coverage: 71.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TRVIFHPVFSVMVSASEDATIKVWDYETGDFERTLKGHT-DSVQDISFDHSGKLLASCSADMTIKLWDFQ
          TRVIFHP.F......SEDATI..W.YETG..E.TLK....DS.QD..FD..GK.LA.C..D.TI.L..FQ
Retrocopy TRVIFHPIFTIIILFSEDATINTWEYETGALEQTLKDQK<DSYQDT*FDQRGKSLACCFTDTTIRL*EFQ

Parental  GFECI-RTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLI
          ......RT..G..HN.SSVAIM.N.D...SA.R..T..MW...TG.CVK.FT....WV.MV.PNQDG.LI
Retrocopy KSLAL<RTIYGYEHNTSSVAIMSNRDFTISALRVTTL*MWDKHTGCCVKAFTSYTKWVCMVPPNQDGKLI

Parental  ASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGSETKKSGKPGPFLLSGSRDKT
          ASCS...T..VW..AT..CK....EH..VVECISW..E.S..S...A....T....KPG..LL.G.RDK.
Retrocopy ASCSHEHTMTVWNTATIYCKSRCCEHKYVVECISWILEGSHPSVVQAMCTDTEQWSKPGINLLYGYRDKM

Parental  IKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADDKTLRVWDYKNKRCMKTLNAHEHFV-TSLDF
          IKMW...T...LM..VGH..WV.GVL.H..G.FI.SCADDK.L....YKN..C.KT.N.H.H.V...L..
Retrocopy IKMWVITTDKSLMSPVGHNDWVCGVLVHPLGTFIMSCADDKNLCL*TYKNGGCIKTINVHNHSV>STLNV

Parental  HKTAPYVVT
          HK...YVVT
Retrocopy HKMTHYVVT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_364 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000007168	2 retrocopies	retro_hsap_2144, retro_hsap_2292,
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,