RetrogeneDB ID: retro_sara_340

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_171549:878..2641(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP15
• Ensembl ID: ENSSARG00000003703
• Aliases: None
• Description: ubiquitin specific peptidase 15 [Source:HGNC Symbol;Acc:12613]

Sequence

>retro_sara_340
AATGTGAAAAACTCAAATTATTGTCTTCCATCATATACTGCTTATAAGAACTACGATTATTCAGAACCTGGAAGAAATAA
TGAGCAGCCAGGCCTTTGTGGCCTGAGTAACTTGGGAAACACCTGTTCATGAACTCAGCTATTCAGTATTTGAGCAACAT
ACCTCCACTTACTGAATATTTCCTCAATGATATGTATCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATGAGAGGGG
AAATAGCTAAGTCTTATGCTGAATTGATCAAACAAATGTGGTCTGGAAAACTTAGCTATGTCACACCAAGAGCCTTTAAG
ACACAAGTAGGATGTTTTGCACCGCAGTTCTCTGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGCTGGA
TGGTCTACATGAGGATTTGAATAGAATTAGGAAAAAAACATACACACAATTAAAAGATGCAGATGGGAGGCCAGAAAAGG
TGGTTGCTGAAGAAGCCTGGGAAAATCATTTAAAAAGAAATGATTCTATCATGGTCGACATATTTCATGGCCTTTTCAAG
TCAACTTCAGTATGTCCTAAATGTGCAAAGATTTCAGTCACATTTGATCCTTTCTGTTACTTGACACTTCCTTTGCCCAT
GAAAAAAGAGCGTACCTTAGAAGTTTACTTAGTTAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTCC
CCAAAATTGGAAACATACAAGATCTTTGTACGGCACTCTCTACTTTGTTAGGCGTACCTGCAGATAAGATGATAGTCACT
GATATATACAATCATAGATTTCACAGAATATTTGCCATGGATGAAAACCTTAGTAGTATTATGGAGCGAGATGATATTTA
TTTGTTTGAGATTAACATCAATAGGACAGAAGATACAGAGCATGTAATTATTCCTGTTTGCCTAAGAGAAAAATTTAGAC
ATTCAAGTTACACACACCATACTGGTTCTTCACTTTTTGGTTAGCCTTTTCTTATAGCAGTACCACGGAACAATACTGAA
GATAAACTCTATAATCTTCTACTTTTGAGAGTGTGCCAGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATC
CCTACATTGCTGTAAGGACCAAAATATTAATGGGAATGGCCCAAATGGCATTCATGAAGAAGGCTTACCAACTGAAATAG
AAACGGTTGAGCCAGATGATGAATTCAGCCAAGATCAAGAACTTCCCTCTGAGAATAAAAGCAGTCAGTCTATAGATTCA
GTTAGAGGAGATAATGATTCTGAAAATGGATTATGTACTGAGGAAAGTTGCAAAGATCAACTCACGGGACACAAAAAGAG
ATTGTTTACATTTCAGTTCAACAATTTAGGCAATACCGATATCAACTACATCAAAGATGACACCCAGCATATAAGATTTG
ATGACAGGCAACTCAGGCTAGATGAAAGATCTTTTCTTGCTTTGGATTGGAATCCTGATTTGAAAAAAAGATACTTTGAT
GAAAATGCTGCTGAGGACTTTGAGAAACATGAAAGTGTGGAATATAAACCTCCCAAAAAACCCTTTGTGAAATTGAAAGA
TTGCATTGAGCTTTTTACAACAAAGGAAAAGCTAGGTGCTGAGGATCCTTGGTATTGTCCAAATTGTAAAGAACATCAAC
AAGCCACAAAGAAATTATATTTATGGTCACTGCCTCCAGTACTTGTGGAACATCTCAAACGGTTTTCTTACAGTCGATAC
ATG

Alignment

ORF - retro_sara_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 59.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTC-FMNSAIQCLSNTPPLTEYFLNDKYQEE
          NVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTC.FMNSAIQ.LSN.PPLTEYFLND.YQEE
Retrocopy NVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTC<FMNSAIQYLSNIPPLTEYFLNDMYQEE

Parental  LNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHED
          LNFDNPLGMRGEIAKSYAELIKQMWSGK.SYVTPRAFKTQVG.FAPQFSGYQQQDCQELLAFLLDGLHED
Retrocopy LNFDNPLGMRGEIAKSYAELIKQMWSGKLSYVTPRAFKTQVGCFAPQFSGYQQQDCQELLAFLLDGLHED

Parental  LNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLT
          LNRIRKK.Y.QLKDADGRP.KVVAEEAWENHLKRNDSI.VDIFHGLFKST.VCP.CAKISVTFDPFCYLT
Retrocopy LNRIRKKTYTQLKDADGRPEKVVAEEAWENHLKRNDSIMVDIFHGLFKSTSVCPKCAKISVTFDPFCYLT

Parental  LPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFA
          LPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTAL.TL.GVPADKMIVTDIYNHRFHRIFA
Retrocopy LPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALSTLLGVPADKMIVTDIYNHRFHRIFA

Parental  MDENLSSIMERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDK
          MDENLSSIMERDDIY.FEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFG.PFLIAVPRNNTEDK
Retrocopy MDENLSSIMERDDIYLFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFG*PFLIAVPRNNTEDK

Parental  LYNLLLLRMCRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSEN
          LYNLLLLR.C.YVKISTETEETEGSLHCCKDQNINGNGPNGIHEEG.P.E.ET.EPDDE.SQDQELPSEN
Retrocopy LYNLLLLRVCQYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGLPTEIETVEPDDEFSQDQELPSEN

Parental  ENSQSEDSVGGDNDSENGLCTEETCKGQLTGHKKRLFTFQFNNLGNTDTNYIKDDTRHIRFDDRQLRLDE
          ..SQS.DSV.GDNDSENGLCTEE.CK.QLTGHKKRLFTFQFNNLGNTD.NYIKDDT.HIRFDDRQLRLDE
Retrocopy KSSQSIDSVRGDNDSENGLCTEESCKDQLTGHKKRLFTFQFNNLGNTDINYIKDDTQHIRFDDRQLRLDE

Parental  RSFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEH
          RSFLALDW.PDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEH
Retrocopy RSFLALDWNPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEH

Parental  QQATKKLDLWSLPPVLVVHLKRFSYSRYM
          QQATKKL.LWSLPPVLV.HLKRFSYSRYM
Retrocopy QQATKKLYLWSLPPVLVEHLKRFSYSRYM

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_340 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 2 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000003703	12 retrocopies	retro_sara_230, retro_sara_303, retro_sara_340 , retro_sara_398, retro_sara_440, retro_sara_491, retro_sara_630, retro_sara_678, retro_sara_683, retro_sara_761, retro_sara_767, retro_sara_81,
Sorex araneus	ENSSARG00000007703	1 retrocopy	retro_sara_550,