RetrogeneDB ID: retro_sara_683

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_258235:43974..45915(-)
• 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_683
GCGGAAGGCGGAGCGGTGGATCTGGACATCCAGCGTTCTGACATCGCGACGCTGCTCAAAATCTCGCTCCGGAAGGGGGA
CACCTGGTACCTAGTTGATAGTCGCTGGTTCAAACAGTGGAAAAAATATGTTGGCTTTGACAGTTGGGACAAATACAAGA
TGGGAGATCAAAATGTATGTCCTTGGACCTATTGATAACTCTGGACTTCTCAAAGATGGTGATGCCCAGTCACTCAAAGA
GCATCTTATCGATGAATTAGATTACATATTATTGCCAACGGAGGGCTGGAATAAACTTGTCAGCTGGTACACGTTGATGG
AAGGGCAAGAACCAATAGCACGGAAGGTGGTTGAACAGGGTATGTCTGTAAAGCACTGCAAAGTAGAAGTATATCTCACA
GAACTGAAGCTTTGTGAAAATGGCAACATGAATAATGTTGTAACTAGAAGATTTAGCAAAGCTGACACAATAGATACAAT
TGAAAAGGAAATCAGAAAAATCTTCAATATTCCAGATGAGAAGGAGACAAGATTGTGGAACAAATGCATGAGTAATACAT
TTGAGCCACTGAATAAGCCAGACAGCACTATTCAGGATGCTGGCTTATATCAAGGACAGGTGTTAGTGATAGAACAGAAA
AATGAAGATGGAACATGGCCAAGGGGTCCTTCTGCTCCTAAGTCCTCAGGTGCATCCAATTTTTCAACTTTACCAAAGAT
ATCTTCTTCATCTCTATCAATTAATTATTACAACATCAAGAACAGAAATGTGAAAAACTCAAATTATTGTCTTCCATCAT
ATACTGCTTATAAGAACTATGATTATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCTGTGGCCTGAGTAACTTG
GGAAACACCTGCTTCATGAACTCAGCTATTCAGTGTTTGAGCAACACACCTCCACTTACTGAATATTTCCTCAATGATAA
GTATCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATTAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCAAAC
AAATGTGGTCTGGAAAATTTAGCTACGTCACACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGCACCGCAGTTCTCT
GGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGTTGGATGGTCTACATGAGGATTTGAATAGAATTAGGAA
AAAACCATACATACAATTAAAAGACGCTGATGGGAGGCCAGAAAAGGTGGTTGCTGAAGAAGCCTGGGAAAATCATTTAA
AAAGAAATGATTCTATCATAGTCGACACATTTCATGGCCTTTTCAAGTCAACTTTAGTATGTCCTGAATGTGCAAAGATT
TCAGTCACATTTGACCCTTTTTGTTACTTGACACTTCCTTTGCCCATGAAAAAAGAGCGTACCTTAGAAGTTTACTTAGT
TAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTCCCCAAAATTGGAAACATACAAGATCTTTGTACGG
CACTCTCTACTTTGTCAGGCGTACCTGCAGATAAGATGATAGTCACTGATATATACAATCATAGATTTCACAGAATATTT
GCCATGGATGAAAACCTTAGTAGTATTATGGAGCGAGATGATATTTATGTGTTTGAGATTAACATCAATAGGACAGAAGA
TACAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAATTTAGACATTCAAGTTACACACACCATACTGGTTCCTCAC
TCTTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTGAAGATAAACTCTTCTACTTTTGAGAATGTGCCGGT
ATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATCCCTACATTGCTGTAATGACCAAAATATTAATGGGAATGGC
CCCAATGGCATCCATGAAGAA

Alignment

ORF - retro_sara_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.78 %
• Parental protein coverage: 66.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEGGAVDLDIQRSDIAKLLKISLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYP-GPIDNSGL
          AEGGAVDLDIQRSDIA.LLKISLRKGDTWYLVDSRWFKQWKKYVGFDSWDKY.MGDQNV.P.GPIDNSGL
Retrocopy AEGGAVDLDIQRSDIATLLKISLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYKMGDQNVCP>GPIDNSGL

Parental  LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCE
          LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGM.VKHCKVEVYLTELKLCE
Retrocopy LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMSVKHCKVEVYLTELKLCE

Parental  NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV
          NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNK.MSNTFEPLNKPDSTIQDAGLYQGQVLV
Retrocopy NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKCMSNTFEPLNKPDSTIQDAGLYQGQVLV

Parental  IEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG
          IEQKNEDGTWPRGPSAPKS.GASNFSTLPKIS.SSLS.NY.NI.NRNVKNSNYCLPSYTAYKNYDYSEPG
Retrocopy IEQKNEDGTWPRGPSAPKSSGASNFSTLPKISSSSLSINYYNIKNRNVKNSNYCLPSYTAYKNYDYSEPG

Parental  RNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW
          RNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLG.RGEIAKSYAELIKQMW
Retrocopy RNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGIRGEIAKSYAELIKQMW

Parental  SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAE
          SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRP.KVVAE
Retrocopy SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPEKVVAE

Parental  EAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPM
          EAWENHLKRNDSIIVD.FHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPM
Retrocopy EAWENHLKRNDSIIVDTFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPM

Parental  QYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTE
          QYKVVVPKIGNIQDLCTAL.TLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTE
Retrocopy QYKVVVPKIGNIQDLCTALSTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTE

Parental  DTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYN-LLLLRMCRYVKISTETEETEG
          DTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKL...LL...........TE..E..G
Retrocopy DTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLFY<LLRMCRYVKISTETEETE--G

Parental  SLHCCKDQNINGNGPNGIHEE
          SLHCC.DQNINGNGPNGIHEE
Retrocopy SLHCCNDQNINGNGPNGIHEE

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_683 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,