RetrogeneDB ID: retro_sara_81

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_2262:5013..7178(+)
• 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_81
ATGGCAGAAGGCAGAGCGGTGGATCTGGACATCCAGCGTTCTGACATCGCGACGCTGCTCAAAATCTTGCTCCGGAAGGG
GGACACCTGGTACCTAGTTGATAGTCGCTGGTTCAAACAGTGGAAAAAATATGTTGGCTTTGACAGTTGGGACAAATACC
AGATGGGAGATCAAAATGTATATCCTGGACCTATTGATAACTCTGGACTTCTCAAAGATGGTGATGCCCAGTCACTCAAA
GAGCATCTTATCGATGAATTGGATTACATATTATTGCCAACGGAGGGCTGGAATAAACTTGTCAGCTGGTACACATTGAT
GGAAGGGCAAGAATCAATAGCACGGAAGGTGCTTGAACAGGGTATGTTTGTAAAGCACTGCAAAATAGAAGTATATCTCA
CAGAACCGAAGCTTTGTGAAAATGGCAACATGAATAATGTTGTAACTAGAAGATTTAGCAAAGCTGACACAATAGATACA
ATTGAAAAGGAAATCAGAAAAATCTTCATTATTCCAGATGAGAAGGAGACAAGATTGTGGAACAAATACATGAGTAATAC
ATTTGAGCCACTGAATAAGCCAGACAGCACTATTCAGGATGCTGGTTTATACCAAGGACAGGTGTTAGTGATAGAACAGA
AAAATGAAGATGGAACATGGCCAAGGGGTCCTTCTGATCCTAAGTCCCCAGGTGCATCCAATTTTTCAACTTTACCAAAG
ATATCTCCTTCATCTCTATCAAATAATTATAACAACATCAACAACAGAAATGTGAAAAACTCAAATTATTGTCTTCCATC
ATATACTGCTTATAAGAACTATGATTATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCTGTGGCCTGAGTAACT
TGGGAAATACCTACTTCATGAACTCAGCTATTCAGTGTTTGAGCAACACACCTCCACATACTGAATATTTCCTCAATGAT
AAGTATCAAGAAGAACTGAATTTTGACAATCCCTTAGGAATGAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCAA
ACAAATGTGGTCTGGAAAATTTAGCTACATCGCACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGCACCGCAGTTCT
CTGGATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGTTGGATGGTCTACATGAGGATTTGAATAGAATTAGG
AAAAAACCATACATACAACTAAAATACGCTGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGCCTGGGAGAATCATTT
AAAAAGAAATGATTCTATCATAGTCGACATATTTCATGGCCTTTTCAAGTCAACTTTAGTATGTCCTGAATGTGCAAAGA
TTTCAGTCACATTTGACCCTTTTTGTTACTTGACACTTCCTTTGCCCATGAAGAGCGTACCTTAGAAGTTTACTTAGTTA
GAATGGATCCACTTACCAAACCTATGCAGTACAAAGTGGTTGTCCCCAAAATTGGAAACATACAAGATCTTTGTACGGCA
CTCTCTACTTTGTCAGGCGTACCTGCAGATAAGATGATAGTCACTGATATATACAATTATAGATTTCACAGAATATTTGC
CATGGATGAAAACCTTAGTAGTATTATGGAGCGAGATGATATTTATGTGTTTGAGATTGACATCAATAGGACAGAAGATA
CAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAATTTAGACATTCAAGTTACACCCACCATACTGGTTCCTCACTT
TTTGGTCAGCCTTTTCTTATAGCAGTACCACGAAACAATACTGAAGATAAACTCTATAATCTTCTACTTTTGAGAATGTG
CCGGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATCCCTACATTGCTGTAAGGACCAAAATATTAATGGGA
ATGGCCCCAATGGCATCCATGAAGAAGGCTCCCCAAGTGAAATGGAAACAGATGAGCCGGATGATGAGTCCAGCCAAGAT
CAAGAACTTCCCTCTGAGAATGAAAACAGTCAGTCTGAAGATTCAGTTGGAGGAGATAATGATTCTGAAAATGGATTATG
TACTGAGGAAACTTGCAAAGGTCAACTCACGGGACACAAAAAGAGATTGTTTACATTCCAGTTCAACAATTTAGGCAATA
CCGAT

Alignment

ORF - retro_sara_81 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.13 %
• Parental protein coverage: 73.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEGGAVDLDIQRSDIAKLLKISLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGL
          MAEG.AVDLDIQRSDIA.LLKI.LRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGL
Retrocopy MAEGRAVDLDIQRSDIATLLKILLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGL

Parental  LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCE
          LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQE.IARKV.EQGMFVKHCK.EVYLTE.KLCE
Retrocopy LKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQESIARKVLEQGMFVKHCKIEVYLTEPKLCE

Parental  NGNMNNVVTRRFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV
          NGNMNNVVTRRFSKADTIDTIEKEIRKIF.IPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV
Retrocopy NGNMNNVVTRRFSKADTIDTIEKEIRKIFIIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLV

Parental  IEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG
          IEQKNEDGTWPRGPS.PKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG
Retrocopy IEQKNEDGTWPRGPSDPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKNYDYSEPG

Parental  RNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW
          RNNEQPGLCGLSNLGNT.FMNSAIQCLSNTPP.TEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW
Retrocopy RNNEQPGLCGLSNLGNTYFMNSAIQCLSNTPPHTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMW

Parental  SGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAE
          SGKFSY..PRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLK.ADGRPDKVVAE
Retrocopy SGKFSYIAPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKYADGRPDKVVAE

Parental  EAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFD-PFCYLTLPLPMKKERTLEVYLVRMDPLTKP
          EAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFD.PF..L........ERTLEVYLVRMDPLTKP
Retrocopy EAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFD<PFLLLDTSFA-HEERTLEVYLVRMDPLTKP

Parental  MQYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVFEININRT
          MQYKVVVPKIGNIQDLCTAL.TLSGVPADKMIVTDIYN.RFHRIFAMDENLSSIMERDDIYVFEI.INRT
Retrocopy MQYKVVVPKIGNIQDLCTALSTLSGVPADKMIVTDIYNYRFHRIFAMDENLSSIMERDDIYVFEIDINRT

Parental  EDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEG
          EDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEG
Retrocopy EDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRMCRYVKISTETEETEG

Parental  SLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEET
          SLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEET
Retrocopy SLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENENSQSEDSVGGDNDSENGLCTEET

Parental  CKGQLTGHKKRLFTFQFNNLGNTD
          CKGQLTGHKKRLFTFQFNNLGNTD
Retrocopy CKGQLTGHKKRLFTFQFNNLGNTD

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_81 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.

---

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,