RetrogeneDB ID: retro_sara_398

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_193038:4857..6795(-)
• 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_398
CTTGGGAACACCTGCTTCATGAACTCAGCTATTCAGTGTTGAGCAACACACCTCCACTTACTGAATATTCCTCAATGATA
AGTATCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATGAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCAAA
CAAATGTGGTCTGGAAAATTTAGCTACGTCACACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGCACCGCAGTTCTC
TGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGTTGGATGGTCTACATGAGGATTTGAATAGAATTAGGA
AAAAACCATACATACAACTAAAAGACGCCGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGCCTGGGAAAATCATTTA
AAAAGAAATGATTCTATCATAGTCGACATATTTCATGGCCTTTTCAAGTCAACTTTAGTATGTCCTGAATGTGCAAAGAT
TTCAGTCACATTTGACCCTTTTTGTTACTTGACACTTCCTTTGCCCATGAAAAAAGAGCATACCTTAGAAGTTTACTTAG
TTAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTCCCCCAAATTGGAAACATACAAGATCTTTGTACG
GCACTCTGTACTTTGTCAGGCGTACCTGCAGATAAGATGATAGTCACTGATATATACAATCATAGATTTCACAGAATATT
TGCCATGGATGAAAACCTTAGTAGTATTATGGAGCGAGATGATATTTATGTGTTTGAGATTAACATCAATAGGACAGAAG
ATACAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAAGTTAGACATTCAAGTTACACACACCATATTGGTTCTTCA
CTTTTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTGAAGATAAACTCTATAATCTACTTTTGAGAATGTG
CCGGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAGGATCCCTACATTGCTGTAAGAACCAAAATATTAATAGGAA
TGGCCCCGATGACATCCATGAAGCAGGCTCACCAAGTGAAATGGAAACAGTTGAGCCGGATGATGAGTCCAGCCAAGATC
AAGAACTTCCCTCTGAGAATGAAAACAGTCAGTCCAAAGATTCAGTTGGAGGAGATAGTGATTCTGAAAATGGATTATGT
ACTGAGGAAACTTGCAAAAGTCAACTCACGGGACACAAAAAGAGATTGTTTACATTCCAGTTCAACAATTTAGGCAATAC
CGATATCAACTACATCAAAGATGACACCCAGCATATAAGATTTGATGATAGGCAGCTTAGGCTAGATGAAAGATCTTTTC
TTGCTTTGGATTGGGATCCTGATTTGAAAAAAAGATACTTTGATGAAACTGCTGCTGAGGACTTTGAGAAACATGAAAGT
GTGGAATATAAACCTCCAAAAAAACCCTTTGGGAAATTGAAAGATTGCATTGAGCTTTTTACAACAAAGGAAAAGCTAGG
TGCTGAAGATCCTTGGTATTGTCCAAATTGTGAAGAATATCAACAAGCCATAAAGAAATTAGATTTATGGTCACTGCCTC
CAGTTCTTGTGGTACATCTCAAACGATTTTCTTACAGTCGATAGATGAGAAATAAATTGGATACATTAGTTGATTTTCCT
ATAAGTGACTTGGATATGTCAGAATTCCTAATTAATCCAAAGGCAGGTCCTTGCCACTATAATTTAATTGCTGTTTCCAA
CCACTATGGGGTGATGGGAAGAGGACATTGTACTGCTTTTGCAAAAAATAAAGATGATGGGAAATGGTACTATTTTGATG
ACAGTAGTATCTCCACAGCATCGAAAGATCAGATTGTGTCCAAAGCCGCGTACGTGCTCTTCTACCAGAGGCAAGACACT
TTCAGTAGAACTAACTGG

Alignment

ORF - retro_sara_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.47 %
• Parental protein coverage: 66.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGNTCFMNSAIQC-LSNTPPLTEY-FLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRA
          LGNTCFMNSAIQC.LSNTPPLTEY.FLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRA
Retrocopy LGNTCFMNSAIQC<LSNTPPLTEY<FLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRA

Parental  FKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRND
          FKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRND
Retrocopy FKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRND

Parental  SIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPMQYKVVVPKIGN
          SIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKE.TLEVYLVRMDPLTKPMQYKVVVP.IGN
Retrocopy SIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKEHTLEVYLVRMDPLTKPMQYKVVVPQIGN

Parental  IQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTEDTEHVIIPVCL
          IQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTEDTEHVIIPVCL
Retrocopy IQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTEDTEHVIIPVCL

Parental  REKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRMCRYVKISTETEETE-GSLHCCKDQNIN
          REK.RHSSYTHH.GSSLFGQPFLIAVPRNNTEDKLYN.LLLRMCRYVKISTETEETE.GSLHCCK.QNIN
Retrocopy REKVRHSSYTHHIGSSLFGQPFLIAVPRNNTEDKLYN-LLLRMCRYVKISTETEETE<GSLHCCKNQNIN

Parental  GNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETCKGQLTGHKKR
          .NGP..IHE.GSPSEMET.EPDDESSQDQELPSENENSQS.DSVGGD.DSENGLCTEETCK.QLTGHKKR
Retrocopy RNGPDDIHEAGSPSEMETVEPDDESSQDQELPSENENSQSKDSVGGDSDSENGLCTEETCKSQLTGHKKR

Parental  LFTFQFNNLGNTDTNYIKDDTRHIRFDDRQLRLDERSFLALDWDPDLKKRYFDENAAEDFEKHESVEYKP
          LFTFQFNNLGNTD.NYIKDDT.HIRFDDRQLRLDERSFLALDWDPDLKKRYFDE.AAEDFEKHESVEYKP
Retrocopy LFTFQFNNLGNTDINYIKDDTQHIRFDDRQLRLDERSFLALDWDPDLKKRYFDETAAEDFEKHESVEYKP

Parental  PKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVHLKRFSYSRYMRDKLDT
          PKKPF.KLKDCIELFTTKEKLGAEDPWYCPNC.E.QQA.KKLDLWSLPPVLVVHLKRFSYSR.MR.KLDT
Retrocopy PKKPFGKLKDCIELFTTKEKLGAEDPWYCPNCEEYQQAIKKLDLWSLPPVLVVHLKRFSYSR*MRNKLDT

Parental  LVDFPISDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYFDDSSVSTASEDQI
          LVDFPISDLDMSEFLINP.AGPC.YNLIAVSNHYG.MG.GH.TAFAKNKDDGKWYYFDDSS.STAS.DQI
Retrocopy LVDFPISDLDMSEFLINPKAGPCHYNLIAVSNHYGVMGRGHCTAFAKNKDDGKWYYFDDSSISTASKDQI

Parental  VSKAAYVLFYQRQDTFSGTGF
          VSKAAYVLFYQRQDTFS.T..
Retrocopy VSKAAYVLFYQRQDTFSRTNW

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_398 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,