RetrogeneDB ID: retro_sara_678

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_257051:7724..10661(+)
• 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_678
ATGGCAGAAGGTGGAGCGGTGGATTTGGATATCCAGTGTTCCGACATGGACACGCTGCTCAAAATCTCGCTCCGGAAGGG
GGACACCTGGTACCTAGTTGATAGTCGCTGGTTCAAACAGTGGAAAAAAGTATGTTGGCTTTGACAGTTGGGTCAAATAC
CAGATGGGAGATCAAAATGTATATCCTGGACCTGTTGATAACTCTGGACTTCTCAAAGATGGTGATGCTCAGTCACTTAA
AGAGCATCTTATTGGTGAATTGGATTACATATTATTGCCAACTCAGGGCTGGAATAAACTTGTCAGCTGGTACACATTGA
TGGAAGGTCAAGAACCAATAGCACGGAAGGTGGTTGAACAGGGTATGTTTGTAAAGCACTGCAAAGTAGAAGTATATCTC
ACAGAACTGAAGCTTTGTGAAAATGGCAACATAAATAATGTTGTTACTGGAAGATTTAGCAAAGCTGACACAATAGATAC
AATTGAAAAGGAAATCAGAAAAATCTTCAATATTCCAGATGAGAAGGAGATGAGATTGTGGAACAAACACATGAGTAATA
CATTTGAGCCACTGAATAAACCAAACAGCACTATTCAGGATGCTGGTTTATACCAAGGACAGGTGTTAGTGATGGAACAG
AAAAATGAAGATGGAACATGGCCAAGGGGTCCTTCTGCTCCTAAGTCCCCAGGTGCTTCCAATTTTTCAACTTTACCAAA
GATATCTCCTTCATCTCTATCAAATAATTATAACAACATCAACAACAGAAATGTGAAAAACTCAAATTATTGTCTTCCAT
CATATACTGCTTATAAGAACTATGATTATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCTGTGGCCTGAGTAAC
TTGGGAAACACCTGCTTCATGAACTCAGCTATTCAGTGTTTGAGCAACACACCTCCACTTACTGAATATTTCCTCAATGA
TAAGTACCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATGAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCA
AACAAATGTGGTCTGGAAAATTTAGCTACGTCACACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGCACCACAGTTC
TCTGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGCTGGATGGTCTACATGAGGATTTGAATAGAATTAG
GAAAAAAAACATACATACAATTAAAAGACACAGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGCCTGGGAAAATCAT
TTAAAAAGAAATGATTCTATCATAGTCGACATATTTCATGGCCTTTTCAAGTCAACTATAGTATGTCCTGAATGTGCAAA
GATTTCAGTCACATTTGATCCTTTTTGTTACTTGACACTTCCATTGCCCACGAAAAAAGAGCGTACCTTAGAAGTTTACT
TAGTTAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGATTGTCCCCAAAACTGGAAATATACAAGATCTTTGT
ACAGCACTCTCTACTTTTTCAGGCGTAGCTGCAGATAAGATGATAGTCACTGATATATACAATCATAGATTTCACAGAAT
ATTTGCCATGGATGAAAACCTTAGTAGTATTATGGAGCAAGATGATATTTATGTGTTTGAGATTAACATCAATAGGACAG
AAGATACAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAATTTAGACATTCAAGTTACACACACCATACTGGTTCT
TCACTTTTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTAAAGATAAACTCTTCTACTTTTGAGAATGTGC
CGGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATCCCTACATTGCTGTAAGGACCAAAATATTAATGGGAA
TGGCCCCAATGGCATCCATGAAGAAGGCTCACCAAGTGAAATGGAAACAGATGAGCCGGATGATGAGTCCAGCCAAGATC
AAGAACTTCCCTCTGAGAATGAAAACAGTCAGTCTGAAGATTCAGTTGGAGGAGATAATGATTCTGAAAATGGATTACGT
ACTGAGGAAACTTGCAAAGGTCAACTCATGGGACACAAAAAGAGATTATTTACATTCCAGTTCAACAATTTAGGCAATAC
CGATATCAACTACATCAAAGATGACACCCAGCATATAAGATTTGATGACAGGCAGCTTAGGCTAGATGAAAGATATTTTC
TTGCTTTGGATTGGGATCCTGATTTGAAAAAAAGATACTTTCATGAAAATGCTGCTGAGAATTTTGAGAAACATGAAAGT
GTGGAATATAAACCTCCCAAAAAACCCTTTGTGAAATTGAAAGATTGCATTGAGCTTTTTACAACAAAGGAAAAGCTAGG
TGCTGAAGATCCTTGGTATTGTCCATATTGTAAAGAACATCAATAAGCCACAAAGAAATTAGATTTATGGTCACTGCCTC
CAATACTTGTGGTACATCTCAAACGATTTTCTTATAGTCGATACATGAGAGATAAATTGGATACCTTAGTTGATTTTCCT
ATAAGTGACTTGGATATGTCAGAATTCCTAATTAATCCAAATGCAGGTCCTTGCTGCTATAATTTGATCGCTGTTTCCAA
CCACTATGGAGGGATGGGAGGAGGACATTATACTGCTTTTGCAAAAAATAAAGATGATGGGAAATGGTACTACTTTGATA
ACAGTAGTGTCTCGAAAGCATCTGAAGATCAGATTGTGTCCAAAGCTGCGTACGTGCTCTTCTACCAGAGGCAAGACACT
TTCAGTGGAACTGGCTTTTCCCCTCTTGACCGGAAACTAAAGGTGCTTCAGCTGCCACAGGCATCCTGTTAGAAAGTGAC
GAAGATAGCAATGATAATGACAATGACATAGAAAATGAAAACTGTATGCACACTAAC

Alignment

ORF - retro_sara_678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEGGAVDLDIQRSDIAKLLKISLRKGDTWYLVDSRWFKQWKK-YVGFDSWDKYQMGDQNVYPGPIDNSG
          MAEGGAVDLDIQ.SD...LLKISLRKGDTWYLVDSRWFKQWKK.YVGFDSW.KYQMGDQNVYPGP.DNSG
Retrocopy MAEGGAVDLDIQCSDMDTLLKISLRKGDTWYLVDSRWFKQWKK>YVGFDSWVKYQMGDQNVYPGPVDNSG

Parental  LLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLC
          LLKDGDAQSLKEHLI.ELDYILLPT.GWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLC
Retrocopy LLKDGDAQSLKEHLIGELDYILLPTQGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLC

Parental  ENGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVL
          ENGN.NNVVT.RFSKADTIDTIEKEIRKIFNIPDEKE.RLWNK.MSNTFEPLNKP.STIQDAGLYQGQVL
Retrocopy ENGNINNVVTGRFSKADTIDTIEKEIRKIFNIPDEKEMRLWNKHMSNTFEPLNKPNSTIQDAGLYQGQVL

Parental  VIEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEP
          V.EQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEP
Retrocopy VMEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEP

Parental  GRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQM
          GRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQM
Retrocopy GRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQM

Parental  WSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIR-KKPYIQLKDADGRPDKVV
          WSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIR....YIQLKD.DGRPDKVV
Retrocopy WSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIR>XXXYIQLKDTDGRPDKVV

Parental  AEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTK
          AEEAWENHLKRNDSIIVDIFHGLFKST.VCPECAKISVTFDPFCYLTLPLP.KKERTLEVYLVRMDPLTK
Retrocopy AEEAWENHLKRNDSIIVDIFHGLFKSTIVCPECAKISVTFDPFCYLTLPLPTKKERTLEVYLVRMDPLTK

Parental  PMQYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININR
          PMQYKV.VPK.GNIQDLCTAL.T.SGV.ADKMIVTDIYNHRFHRIFAMDENLSSIME.DDIYVFEININR
Retrocopy PMQYKVIVPKTGNIQDLCTALSTFSGVAADKMIVTDIYNHRFHRIFAMDENLSSIMEQDDIYVFEININR

Parental  TEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYN-LLLLRMCRYVKISTETEET
          TEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNT.DKL...LL...........TE..E.
Retrocopy TEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTKDKLFY<LLRMCRYVKISTETEETE-

Parental  EGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTE
          .GSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGL.TE
Retrocopy -GSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLRTE

Parental  ETCKGQLTGHKKRLFTFQFNNLGNTDTNYIKDDTRHIRFDDRQLRLDERSFLALDWDPDLKKRYFDENAA
          ETCKGQL.GHKKRLFTFQFNNLGNTD.NYIKDDT.HIRFDDRQLRLDER.FLALDWDPDLKKRYF.ENAA
Retrocopy ETCKGQLMGHKKRLFTFQFNNLGNTDINYIKDDTQHIRFDDRQLRLDERYFLALDWDPDLKKRYFHENAA

Parental  EDFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVHLKR
          E.FEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCP.CKEHQ.ATKKLDLWSLPP.LVVHLKR
Retrocopy ENFEKHESVEYKPPKKPFVKLKDCIELFTTKEKLGAEDPWYCPYCKEHQ*ATKKLDLWSLPPILVVHLKR

Parental  FSYSRYMRDKLDTLVDFPISDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYF
          FSYSRYMRDKLDTLVDFPISDLDMSEFLINPNAGPC.YNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYF
Retrocopy FSYSRYMRDKLDTLVDFPISDLDMSEFLINPNAGPCCYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYF

Parental  DDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGFFPLDR-ETKGASAATSIPLESDEDSNDNDNDIENKN
          D.SSVS.ASEDQIVSKAAYVLFYQRQDTFSGTGF.PLDR.ETKGASAAT.I.LESDEDSNDNDNDIEN.N
Retrocopy DNSSVSKASEDQIVSKAAYVLFYQRQDTFSGTGFSPLDR<ETKGASAATGILLESDEDSNDNDNDIENEN

Parental  CMHTN
          CMHTN
Retrocopy CMHTN

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_678 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,