RetrogeneDB ID: retro_sara_266

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_137982:5677..6718(-)
• 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_266
AAAATTAGGGATCTAGAATTCCTACTTCAACGTGCTTCAGAAGAATTGAAATAAAATCAGTGCCTTGTACGAAGACAAAA
TCTAATATAATGGGTTCCCCTTGTTACTGAAAAATATTCTCTGAATGGACACAGTGGCCAGATTACTAGAGTAATTTTCC
ATCCTGTGCTCACTCTTATTGCTTCTTCCTCCGAAAATGCTACAATTCGAGTCTGGGATTCTGAGACTGGGGCTTTAAAA
CAAACCCTTAAAGGCCATTCAGATACTATTCATGATATTTCATTTGACAACAGCGGGAAAGTGCTTGCCTCCTGCTCTGC
AGATGGTATCATCAAAGTGTGGGATTTTCAGCGTTCTTTCTGTGTTAAAACCATCCACGGCCATAATCAAGATGTTTCTT
CAGTGGCCTTCATGCCCAATGGAGAGTATATAATCTCTGCCTCACGGGACACAACCTTAAAGATGTGGGACATACAGAGT
GGCTACTGTGTAAAGATATTCACTGGCCACACAAAATGGGTACGTATGGCACGACCAAATCAGGATGGCACGCTGATTGC
AAGCTGTTCGCATGACCACACTGTGCGTATTTGGGATGCGAATAGTATGCAGTGCAGGAACGAGCTTCGGGAACATGAGC
ATGTGGTGGAGTGCATTTCTTGGGTGCCAATAAATGCACATTCTTCTATTTTGGAAGCAACTGGTGTTGAGACTAACACA
TGGGACCAGTCGGAACTCTTTTTACTATCTGGTTCAAGAGATAAGATGATTAAGATGTGGAATATAAGCACTGGCAAGAG
CCTTATAACCCTAGTGGGTCATGATAACTGGGTTCGTGGGGTCTTTGTCCTTCCCCTCGGTACTTTCATCATAAGCTGTG
GGGATGACAAGACTATACGTATATGGAATTATAAGAAAAGACAATGCATTAAAACTCTCAAGGCACACAATCATTTTGTC
TCCACCGTGGATGTCCACAAGATGACCCAGTATGTGGTAACTGGCAGCTGTGATCAAACCATCAAGTTGTGGGAGTGCCA
G

Alignment

ORF - retro_sara_266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.52 %
• Parental protein coverage: 86.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPVFSVMVSASEDATIK
          ....LE..L..A.EE......L........W.P...EKY.L.GH....TRVIFHPV.....S.SE.ATI.
Retrocopy KIRDLEFLLQRASEELK*NQCLVRRQNLI*WVPLVTEKYSLNGHSGQITRVIFHPVLTLIASSSENATIR

Parental  VWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDFQGFECIRTMHGHDHNVSSVAIMPN
          VWD.ETG....TLKGH.D...DISFD.SGK.LASCSAD..IK.WDFQ...C..T.HGH...VSSVA.MPN
Retrocopy VWDSETGALKQTLKGHSDTIHDISFDNSGKVLASCSADGIIKVWDFQRSFCVKTIHGHNQDVSSVAFMPN

Parental  GDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIASCSNDQTVRVWVVATKECKAELR
          G..I.SASRD.T.KMW..Q.GYCVK.FTGH..WVRM.RPNQDGTLIASCS.D.TVR.W......C..ELR
Retrocopy GEYIISASRDTTLKMWDIQSGYCVKIFTGHTKWVRMARPNQDGTLIASCSHDHTVRIWDANSMQCRNELR

Parental  EHEHVVECISWAPESSYSSISEATGSETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRG
          EHEHVVECISW.P....SSI.EATG.ET........FLLSGSRDK.IKMW..STG..L.TLVGHDNWVRG
Retrocopy EHEHVVECISWVPINAHSSILEATGVETNTWDQSELFLLSGSRDKMIKMWNISTGKSLITLVGHDNWVRG

Parental  VLFHSGGKFILSCADDKTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR
          V.....G.FI.SC.DDKT.R.W.YK...C.KTL.AH.HFV...D.HK...YVVTGS.DQT.K.WEC.
Retrocopy VFVLPLGTFIISCGDDKTIRIWNYKKRQCIKTLKAHNHFVSTVDVHKMTQYVVTGSCDQTIKLWECQ

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_266 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,