RetrogeneDB ID: retro_sara_491

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_225643:105845..107975(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000005903
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_491
ATGGCAGAAGGCGGAGCGGTGGATCTGGACATCCAGCGTTCGGACATCGCGACGCTGCTCAAAATCTCGCTCCGGAAGGG
GGACACCTGGTACCTAGTTGATAGTCGCTGGTTCAAACAGTGCAAAAAATATGTTGGCTTTGACAGTTGGGACAAATACC
AGATGGGAGATCAAAATGTATATCCTGGACCTATTGATAACTCTGGACTTCTCAAAGATGGTGATGCCCAGTCACTCAAA
GAGCATCTTATTGATGAATTGGATTACATATTATTGCCAATGGAGGGCTGGAATAAACTTGTCAGCTGGTACACGTTGAT
GGAAGGGCAAGAACCAATAGCACGGAAGGTGGTTGAACAGGGTCTGTTTGTAAAGCACTGCAAAGTAGAAGTATATCTCA
CAGAACTGAAGCTTTGTGAAAATGGCAACATGAATAATGTTGTAACTAGAAGATTTAGCAAAGCTGACACAATAGATACA
ATTGAAAAGGAAATCAGAAAAATCTTCAATATTCCAGATGAGAAGGAGACAAGATTGTGGAACAAATACATGAGTAATAC
ATTTGAGCCACTGAATAAGCCAGACAGCACTATTCAGGATGCTGGTTTATACCAAGGACAGGTGTTAGTGATAGAACAGA
AAAATGAAGATGGAACATGGCCAAGGGGTCCTTCTGCTCCTAAGTCCCCAGGTGCATCCAATTTTTCAACTTTACCAAAG
ATATCTCCTTCATCTCTATCAAATAATTATAACAACATCAACAACAGAAATGTGAAAAACTCAAATTATTGTCTTCCATC
ATATACTGCTTATAAGAACTATGATTATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCTGTGGCCCGAGTAACT
TGGGAAACACCTGCTTCATGAACTCAGCTATTCAGTGTTTGAGCAACACACCTCCACTTACTGAATGTTTCCTCAATGAT
AAGTATCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATGAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCAA
ACAAATGTGGTCTGGAAAATTTAGCTACGTCACACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGCACCGCAGTTCT
CTGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGTTGGATGGTCTACATGAGGATTTGAATAGAATTAGG
AAAAAACCATACATACAACTAAAAGACGCCGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGCCTGGGAAAATCATTT
AAAAAGAAATGATTCTATCATAGTCGACATATTTCATGACCTTTTCAAGTCAACTTTAGTATGTCCTGAATGTGCAAAGA
TTTCAGTCACATTTGACCCTTTTTGTTACTTGACACTTCCTTTGCCCATGAAAAAAGAGCATACCTTAGAAGTTTACTTA
GTTAGAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTCCCCAAAATTGGAAACATACAAGATCTTTGTAC
GGCACTCTGTACTTTGTCAGGCGTACCTGCAGATAAGATGATAGTCACTGATATATACAATCATAGATTTCACAGAATAT
TTGCCATGGATGAAAACCTTAGTAGTATTATGGAGCGAGATGATATTTATGTGTTTGAGATTAACATCAATAGGACAGAA
GATACAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAATTTAGACATTCAAGTTACACACACCATACTGGTTCCTC
ACTTTTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTGAAGATAAACCCTATAATCTTCTACTTTTGAGAA
TGTGCCGGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATCCCTACATTGCTGTAAGGACCAAAATAGTAAT
GGGAACGGCCCCAATGGCATCCATGAAGAAGGCTCCCCAAGTGAAATGGAAACAGATGAGCCAGATGATGAGTCCAGCCA
AGATCAAGAACTTCCCTCTGAGAATGAAAACAGTCAGTCTGAAGATTCAGTTGGAGGAGATAATGATTCTGAAAATGGAT
TATGTACTGAGGAAACTTGCAAAGGTCAACTCACGGGACACACAAAAAGA

Alignment

ORF - retro_sara_491 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.45 %
• Parental protein coverage: 72.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEGGAVDLDIQRSDIAKLLKISLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGL
          MAEGGAVDLDIQRSDIA.LLKISLRKGDTWYLVDSRWFKQ.KKYVGFDSWDKYQMGDQNVYPGPIDNSGL
Retrocopy MAEGGAVDLDIQRSDIATLLKISLRKGDTWYLVDSRWFKQCKKYVGFDSWDKYQMGDQNVYPGPIDNSGL

Parental  LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCE
          LKDGDAQSLKEHLIDELDYILLP.EGWNKLVSWYTLMEGQEPIARKVVEQG.FVKHCKVEVYLTELKLCE
Retrocopy LKDGDAQSLKEHLIDELDYILLPMEGWNKLVSWYTLMEGQEPIARKVVEQGLFVKHCKVEVYLTELKLCE

Parental  NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV
          NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV
Retrocopy NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV

Parental  IEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG
          IEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG
Retrocopy IEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG

Parental  RNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW
          RNNEQPGLCG.SNLGNTCFMNSAIQCLSNTPPLTE.FLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW
Retrocopy RNNEQPGLCGPSNLGNTCFMNSAIQCLSNTPPLTECFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW

Parental  SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAE
          SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAE
Retrocopy SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAE

Parental  EAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVRMDPLTKPM
          EAWENHLKRNDSIIVDIFH.LFKSTLVCPECAKISVTFDPFCYLTLPLPMKKE.TLEVYLVRMDPLTKPM
Retrocopy EAWENHLKRNDSIIVDIFHDLFKSTLVCPECAKISVTFDPFCYLTLPLPMKKEHTLEVYLVRMDPLTKPM

Parental  QYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTE
          QYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTE
Retrocopy QYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRTE

Parental  DTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEGS
          DTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDK.YNLLLLRMCRYVKISTETEETEGS
Retrocopy DTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKPYNLLLLRMCRYVKISTETEETEGS

Parental  LHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETC
          LHCCKDQN.NGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETC
Retrocopy LHCCKDQNSNGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEETC

Parental  KGQLTGHKKR
          KGQLTGH.KR
Retrocopy KGQLTGHTKR

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_491 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,