RetrogeneDB ID: retro_sara_440

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_208167:921..3096(-)
• 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_440
AACGTGAAAAACTCAAATTATTGTCTTCCATCATATACTGCTTATAAGAACTATGATTATTCAGAACCTGGAAGAAATAA
TGAGCATCCAGGCCTCTGTGGCCTGAGTAACTTGGGAAACACCTGCTTCATGAACTCAGCTATTCAGTGTTTGAGCAACA
CACCTCCACTTACTGAATATTTCCTCAATGATAAGTATCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATGAGAGGT
GAAATAGCTAAGTCTTATGCTGAATTGATCAAACAAATGTGGTCTGGAAAATTTAGCTACGTCACACCAAGAGCCTTTAA
GACACAAGTAGGACGTTTTGCACCGCAGTTCTCTGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGTTGG
ATGGTCTACATGAGGATTTGAATAGAATTAGGAAAAAACCATACATACAATTAAAAGACGCCGATGGGAGGCCAGATAAG
GTGGTTGCTGAAGAAGCCTGGGAGAATCATTTAAAAAGAAATGATTCTATCATAGTCGACATATTTCATGGCCTTTTCAA
GTCAACTTTAGTATGTCCTGAATGTGCAAATATTTCAGTCACATTTGACCCTTTTTGTTACTTGACACTTCCTTTGCCCA
TGAAAAAAGAGCATACCTTAGAAGTTTACTTAGTTAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTC
CCCAAAATTGGAAACATACAAGATCTTTGTACGGCACTCTCTACTTTGTCAGGCGTACCTGCAGATAAGATGATAGTCAC
TGATATATACAATCATAGATTTCACAGAATATTTGCCATGGATGAAAACCTTAGTAGTATTATAGAGCGAGATGATATTT
ATGTGTTTGAGATTAACATAAATAGGACAGAAGATACAGAGCATGTAATTACTCCTGTTTGCCTAAGAGAAAAATTTAGA
CATTCAAGTTACACACACCATACTGGTTCCTCACTTTTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTGA
AGATAAACTCTATAATCTTCTACTTTTGAGAATGTGCCAGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGAT
CCCTACATTGCTGTAAGGACCAAAATATTAATGGGAACGGCCCCAATGGCATCCATGAAGAAGGCTCACCAAGTGAAATG
GAAAGAGATGAGCTGGATGATGAGTCCAGCCAAGATCAAGAACTTCCCTCTGAGAATGAAAACAGTCAGTCTGAAGATTC
AGTTGGAGGAGATAATGATTCTAAAAATGGATTATGTACTGAGGAAACTTGCAAAGGTCAACTCACGGGACACAAAAAGA
GATCGTTTACATTCCAGTTCAACAATTTAGGCAATACCGATACCAACTACATCAAAGAGGACACCCGGCATATAAGATTT
GATGACAGGCAGCTTAGGCTAGATGAAAGATCTTTTCTTGCTTTGGATTGGGATCCTGATTTGAAAAAAAGATACTTTGA
TGAAAATGCTGCTGAGGACTTTGAGAAACATGAAAGTGTGGAATATAAGCCTCCCAAAAAACCCTTTGTGAAATTGAAAG
ATTGCATTGAGCTTTTTACAACAAAGGAAAAGCTAGGTGCTGAGGATCCTTGGTATTGTCCAAATTGTAAAGAACATCAA
CAAGCCACAAAGAAATTATATTTATGGTCACTGCCTCCAGTACTTGTGGAACATCTCAAACGGTTTTCTTACAGTCGATA
CATGAGAGATAAATTGGATACCTTAGTTGACTTTCCTATAAGTGACTTGGATATGTCAGAATTCCTGATTAATCCAAACG
CAGGTCCTTGCCGCTATAATTTAATCGCTGTTTCCAAACACTATGGAGGGAAGGGAGGAGGACATTATACTGCTTTTGCC
AAAAATAAAGATGATGGGAAATGGTACTACTTTGATGACAGTAGTGTCTCCACAGCATCTGAAGATTAGATTGTGTCCAA
AGCTGCATACGTGCTCTTCTACCAGAGGCAAGACACTTTCAGTGGAACTGGCTTTTTCCCTCTTGACTGAGAAACTAAAG
GTGCTTCAGCTGCCACAAGCATCCCATTAGAAAGTGACAGAGATAGCAATGATAATGACAATGACATAGAAAACGAAAAC
TGTATGCACACTAAC

Alignment

ORF - retro_sara_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.24 %
• Parental protein coverage: 73.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEEL
          NVKNSNYCLPSYTAYKNYDYSEPGRNNE.PGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEEL
Retrocopy NVKNSNYCLPSYTAYKNYDYSEPGRNNEHPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEEL

Parental  NFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDL
          NFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDL
Retrocopy NFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDL

Parental  NRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTL
          NRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECA.ISVTFDPFCYLTL
Retrocopy NRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECANISVTFDPFCYLTL

Parental  PLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAM
          PLPMKKE.TLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTAL.TLSGVPADKMIVTDIYNHRFHRIFAM
Retrocopy PLPMKKEHTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALSTLSGVPADKMIVTDIYNHRFHRIFAM

Parental  DENLSSIMERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKL
          DENLSSI.ERDDIYVFEININRTEDTEHVI.PVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKL
Retrocopy DENLSSIIERDDIYVFEININRTEDTEHVITPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKL

Parental  YNLLLLRMCRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENE
          YNLLLLRMC.YVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEME.DE.DDESSQDQELPSENE
Retrocopy YNLLLLRMCQYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMERDELDDESSQDQELPSENE

Parental  NSQSEDSVGGDNDSENGLCTEETCKGQLTGHKKRLFTFQFNNLGNTDTNYIKDDTRHIRFDDRQLRLDER
          NSQSEDSVGGDNDS.NGLCTEETCKGQLTGHKKR.FTFQFNNLGNTDTNYIK.DTRHIRFDDRQLRLDER
Retrocopy NSQSEDSVGGDNDSKNGLCTEETCKGQLTGHKKRSFTFQFNNLGNTDTNYIKEDTRHIRFDDRQLRLDER

Parental  SFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQ
          SFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQ
Retrocopy SFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQ

Parental  QATKKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPISDLDMSEFLINPNAGPCRYNLIAVSNHYGG
          QATKKL.LWSLPPVLV.HLKRFSYSRYMRDKLDTLVDFPISDLDMSEFLINPNAGPCRYNLIAVS.HYGG
Retrocopy QATKKLYLWSLPPVLVEHLKRFSYSRYMRDKLDTLVDFPISDLDMSEFLINPNAGPCRYNLIAVSKHYGG

Parental  MGGGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGFFPLDRETKGASAATS
          .GGGHYTAFAKNKDDGKWYYFDDSSVSTASED.IVSKAAYVLFYQRQDTFSGTGFFPLD.ETKGASAATS
Retrocopy KGGGHYTAFAKNKDDGKWYYFDDSSVSTASED*IVSKAAYVLFYQRQDTFSGTGFFPLD*ETKGASAATS

Parental  IPLESDEDSNDNDNDIENKNCMHTN
          IPLESD.DSNDNDNDIEN.NCMHTN
Retrocopy IPLESDRDSNDNDNDIENENCMHTN

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_440 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,