RetrogeneDB ID: retro_sara_588

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_236075:4099..4974(-)
• 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_588
TCCAGAGTCATAGCTGATTACCTTTGTTCAAATGGCTTTGAACAGGCATATTACATTTTTAAAATGTAAGCTGAATTGGA
TATGAGTCAAGAATTAGATAAGAAATATGCCAGACTTTTGGAAAAGAAATGAACATCCAGCATTAGTTTATAGAAGAAGT
TTATGGATTTAGAATTAAAAATAAACTAAGAAAAAGAAGAACCGAAAACAATTGTACACCTTGTACAGACACAAGATCTG
ATAGAATGGGTACCCCTTGTTCTAGAAAAATATGCATTCAATGACCACAGGAGCCTGGTTTCTAGCAAGATTTTCCACCC
CGTATTCATCATTATGGTTTCAGCTTCAGGAAACGCAACAATAAAAACATGGGATTATGAGACTGGAACTTTGGAACAAA
CTCTTAAAGCACATACAGACTCAGATTAGTGTATTTCACTTGATCAAAGTGGGAAATCACTTGCCTCCTGCTCTGTAGAT
ACTGTCATCAAATTGTGGGATTTTCAGAGTTGTCTCCTCATTATAACCAGCTACAGTCATGATCATGATGTTTCTTTAGT
GGCCTCATGCCCATTGGAGGTTGTATAGTTTTTGCCTCACAGGATAAAACCTTAAAAATGTGGGATATACACAATGGCCA
CTGCATGAAGATATTCACAGGCCACATGAAGTGGGTATGTATGATGCAACTAAATCAAGATGGCACACTGATAACAAGCT
AGTCTCAAGACTGTACTGTGAGAGTCTGGGTGATAGCAACTACACAGTGCAAGAAGGAGCTTCAGGAACATCAATATGCT
GTGGAATGCATATCTTGGGCTCCAGAAAATGCACATCTTTCCACTGTGGAAGCAAGAGATTCTCATACTGAAAAA

Alignment

ORF - retro_sara_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.41 %
• Parental protein coverage: 73.18 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NRAIADYLRSNGYEEAYSVFKKEAELDMNEELDKKYACLLEKKCTSVIRLQKRVMELESKLNEAKEEFTS
          .R.IADYL.SNG.E.AY..FK..AELDM..ELDKKYA.LLEKK.TS.I.L.K..M.LE.K.N..KEE...
Retrocopy SRVIADYLCSNGFEQAYYIFKM*AELDMSQELDKKYARLLEKK*TSSISL*KKFMDLELKIN*EKEEPKT

Parental  GGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPVFSVMVSASEDATIKVWDYETGDFERTLKGHTD
          ...L.Q..D..EW.P...EKYA...HRS.V...IFHPVF..MVSAS..ATIK.WDYETG..E.TLK.HTD
Retrocopy IVHLVQTQDLIEWVPLVLEKYAFNDHRSLVSSKIFHPVFIIMVSASGNATIKTWDYETGTLEQTLKAHTD

Parental  SVQDISFDHSGKLLASCSADMTIKLWDFQGFECIRTMHGHDHNVSSVA-IMPNGDHIVSASRDKTIKMWE
          S...IS.D.SGK.LASCS.D..IKLWDFQ....I.T...HDH.VS.VA..MP.G..IV.AS.DKT.KMW.
Retrocopy SD*CISLDQSGKSLASCSVDTVIKLWDFQSCLLIITSYSHDHDVSLVA<LMPIGGCIVFASQDKTLKMWD

Parental  VQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSY
          ...G.C.K.FTGH..WV.M...NQDGTLI.S.S.D.TVRVWV.AT..CK.EL.EH...VECISWAPE...
Retrocopy IHNGHCMKIFTGHMKWVCMMQLNQDGTLITS*SQDCTVRVWVIATTQCKKELQEHQYAVECISWAPENAH

Parental  SSISEATGSETKK
          .S..EA..S.T.K
Retrocopy LSTVEARDSHTEK

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_588 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 ,