RetrogeneDB ID: retro_sara_630

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_244848:3642..5897(-)
• 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_630
AGCTGGTACACGTGATGGAAGGGCAAGAACCAATAGCACGAAAGGTGGTTGAACAGGGTATGTCTGTAAAGCACTGCAAA
GTAGAAGTATATCTCACAGAACTGAAGCTTTGTGAAAATGGCAACATGAATAATGTTGTAACTAGAAGATTTAGCAAAGC
TGACACAATAGATACAATTGAAAAGGAAATCAGAAAAATCTTCAATATTCCAGATGAGAAGGAGATAAGATTGTGGAACA
AATACATGAGTAATACATTTGAGCCACTGAATAAGCCAGACAGCACTATTCAGGATGCTGGTTTATACCAAGGACAGGTG
TTAGTGATAGAACAGAAAAATGAAGATGGAACATGGCCAAGGGGTCCTTGTGCTCCTAAGTCCCCAGGTGCATCCAATTT
TTCAACTTTACCAAAGATATCTCCTTCATCTCTATCAAATAATTATACAACATCAACAACAGAAATGTGAAAAACTCAAA
TTATTGTCTTCCATCATATACTGCTTATAAGAACTATGATTATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCT
GTGGCCTGAGTAACTTGGGAAACATCTGCTTCATGAACTCAGCTATTCAGTGTTTGAACAACACACCTCCACTTACTGAA
TATTTCCTCAATGATAAGTATCAAGAAGAACTGACTTTTGACAATCCCTTAGGAATGAGAGGTGAAATAGCTAAGTCTTA
TGCTGAATTGATCAAACAAATGTGGTCTGGAAAATTTAGCTACGTCACACCAAGAGCCTTTAAGACGCAAGTAGGACGTT
TTGCACCGCAGTTCTCTGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGCTGGATGGTCTACATGAGGAT
TTGAATAGAATTAGGAAAAAACCATACATACAATTAAAAGACGCCGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGC
CTGGGAAAATCATTTAAAAAGAAATGATTCTATCATAGTCGACATATTTCATGGCCTTTTCAAGTCAACTTTAGTATGTC
CTGAATGTGCAAATATTTCAGTCACATTTGATCCTTTTTGTTACTTGACACTTCCTTTGCCCATGAAAAAAGAGCATACC
TTAGAAGTTTACTTAGTTAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTCCCCAAAATTGGAAACAT
ACAAGATCTTTGTACGGCACTCTGTACTTTGTCAGGCGTACCTGCAGATAAGATGATAGTCACTGATATATGCAATCATA
GATTCCACAGAATATTTGCCATGGATGAAAACCTTAGTAGTATTATGGAATGAGATGATATTTATGTGTTTGAGATTAAC
ATCAATAGGACAGAAGATACAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAATTTAGACATTCAAGTTACACACA
CCATACTGGTTCCTCACTCTTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTGAAGATAAACTCTATAATC
TTCTACTTTTGAGAATGTGACGGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATCCTTACATTGCTGTAAG
GACCAAAATATTAATGGGAACGGCCCCAGTGGCATCCATGAAGAAGGCTCACCAAGTAAAATGGAAACAGATGAGCCGGA
TGATGAGTCCAGCCAAGATCAAGAACTTCCCTCTGAGAATGAAAACAGTCAGTCTGAAGATTCAGTTGGAGGAGATAATG
ATTCTGAAAATGGATTATGTACTGAGGAAACTTGCAAAGGTCAACTCACGGGACACAAAAAGATATTGTTTACATTCCAG
TTCAACAATTTAGGCAATATCGATACCAACTACATCAAAGATGACACTAGGCATATAAGATTTGATGACAGGCAGCATAG
GCTAGATGAAAGATCTTTTCTTGCTTTGGATTGGGATCCTGATTTGAAAAAAAGATACTTTGATGAAAATGCTGATGAGG
ACTTTGAGAAACATGAAAGTGTGGAATATAAGCCTCCAAAAAAACCCTTTGTGAAATTGAAAGATTGCATTGAGCTTTTT
ACAACAAAGGAAAGCTAGGTGCTTATGATCCTTGGTATTGTCCAAATTGTAAAGAACATCAACAAGCCACAAAGAAATTA
GATTTACGGTCATTGCCTCCAGTACTTATGGTACATCTCAAATGATTTTCTTACAGTTGATACATGAGAGATAAATTGGA
TCCTTAGTTGACTTC

Alignment

ORF - retro_sara_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.17 %
• Parental protein coverage: 76.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SWYT-LMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFN
          SWYT..MEGQEPIARKVVEQGM.VKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFN
Retrocopy SWYT<VMEGQEPIARKVVEQGMSVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFN

Parental  IPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPRGPSAPKSPGASNFSTLPK
          IPDEKE.RLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPRGP.APKSPGASNFSTLPK
Retrocopy IPDEKEIRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPRGPCAPKSPGASNFSTLPK

Parental  ISPSSLSNNYN-NINNRNVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSN
          ISPSSLSNNY..NINNRNVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGN.CFMNSAIQCL.N
Retrocopy ISPSSLSNNYT<NINNRNVKNSNYCLPSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNICFMNSAIQCLNN

Parental  TPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQ
          TPPLTEYFLNDKYQEEL.FDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQ
Retrocopy TPPLTEYFLNDKYQEELTFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQ

Parental  DCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCP
          DCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCP
Retrocopy DCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCP

Parental  ECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADK
          ECA.ISVTFDPFCYLTLPLPMKKE.TLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADK
Retrocopy ECANISVTFDPFCYLTLPLPMKKEHTLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADK

Parental  MIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLF
          MIVTDI.NHRFHRIFAMDENLSSIME.DDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLF
Retrocopy MIVTDICNHRFHRIFAMDENLSSIME*DDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLF

Parental  GQPFLIAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETD
          GQPFLIAVPRNNTEDKLYNLLLLRM.RYVKISTETEETEGSLHCCKDQNINGNGP.GIHEEGSPS.METD
Retrocopy GQPFLIAVPRNNTEDKLYNLLLLRM*RYVKISTETEETEGSLHCCKDQNINGNGPSGIHEEGSPSKMETD

Parental  EPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETCKGQLTGHKKRLFTFQFNNLGNTDTNYIKD
          EPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETCKGQLTGHKK.LFTFQFNNLGN.DTNYIKD
Retrocopy EPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETCKGQLTGHKKILFTFQFNNLGNIDTNYIKD

Parental  DTRHIRFDDRQLRLDERSFLALDWDPDLKKRYFDENAAEDFEKHESVEYKPPKKPFVKLKDCIELFTTKE
          DTRHIRFDDRQ.RLDERSFLALDWDPDLKKRYFDENA.EDFEKHESVEYKPPKKPFVKLKDCIELFTTKE
Retrocopy DTRHIRFDDRQHRLDERSFLALDWDPDLKKRYFDENADEDFEKHESVEYKPPKKPFVKLKDCIELFTTKE

Parental  -KLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVHLKRFSYSRYMRDKLD-TLVDF
          .KLGA.DPWYCPNCKEHQQATKKLDL.SLPPVL.VHLK.FSYS.YMRDKLD..LVDF
Retrocopy <KLGAYDPWYCPNCKEHQQATKKLDLRSLPPVLMVHLK*FSYS*YMRDKLD<SLVDF

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_630 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,