RetrogeneDB ID: retro_sara_275

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_143031:7277..7922(-)
• 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_275
ACATCTGTTATTAGGTTAAAGAAGGTTGTTGATTTAGAATTAAAATTAAACTAAGAAAAAGAACACCTGAAAGCAAGTTT
GTTGTTTAGAAAGAATCAAGATCAGATAGAGTAGGCACCATTTTTTACTAAAAAATATGCACTTAATGGAACCAAGGGTC
TGGTTACAAAAGTGATTCTTCACCCCAAGCTCACTATTATCATTTCTTCCTAGGAAGATGATACAATTAAAGCCTGGGAT
TATAAAAGTGGAGCTTTGGAAACAACATTGAAAGGCCACACAGACTCAGTTCAGGATATTTCATTTGACCAGAATAAGAA
ATTACTCACCTCCTGCTCTGCAGACACAAACATCAAACTGTGGAAATTTCGGAATTCTCTCTGCATTCGAATCATCTATG
GCCAGGAGCACAATGCTTCTTCTTTGGCCATCATGCACAATGAAGATTTTATCATATCAGCCTCATGAGATACAACCTTA
GCGATGTGGGATATACACACCGGCTACTGCATTAAAACATTCACTGGCCACAAAAAGTGGATATGTATGGTATGTCCAAA
ACAGGACGGCACACTGATAGCAAGCTGTTCGCATGACCACACCATGCATGTTTGGGATACAGCCACTGTGCAGTGTAAGA
GTGAG

Alignment

ORF - retro_sara_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.48 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSVIRLQKRVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPVFSVMVS
          TSVIRL.K.V..LE.KLN..KE............D..E..P....KYAL.G....VT.VI.HP......S
Retrocopy TSVIRL-KKVVDLELKLN*EKEHLKASLLFRKNQDQIE*APFFTKKYALNGTKGLVTKVILHPKLTIIIS

Parental  ASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDFQGFECIRTMHGHDHNV
          ..ED.TIK.WDY..G..E.TLKGHTDSVQDISFD...KLL.SCSAD..IKLW.F....CIR...G..HN.
Retrocopy S*EDDTIKAWDYKSGALETTLKGHTDSVQDISFDQNKKLLTSCSADTNIKLWKFRNSLCIRIIYGQEHNA

Parental  SSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRVWVVAT
          SS.AIM.N.D.I.SAS.D.T..MW...TGYC.KTFTGH..W..MV.P.QDGTLIASCS.D.T..VW..AT
Retrocopy SSLAIMHNEDFIISAS*DTTLAMWDIHTGYCIKTFTGHKKWICMVCPKQDGTLIASCSHDHTMHVWDTAT

Parental  KECKAE
          ..CK.E
Retrocopy VQCKSE

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_275 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,