RetrogeneDB ID: retro_sara_230

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_114210:1..1503(-)
• 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_230
GCTACTATTCAGGATGCTGGTTTATACCAAGGACAGGTGTTAGCGATAGAACAGAAAAATGAAGATGGAACATGGCCAAG
GGGTCCTTCTGCTCCTAAGTCCCCAGGTGCATCCAATTTTTCAACTTTACCAAAGATATCTCCTTCATCTCTATCAAATA
ATTATAACAACATCAACAACAGAAATGTGAAAAACTCAAATTATTGTCTTCCATCATATACTGCTTATAAGAACTATGAT
TATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCTGTGGCCTGAGTAACTTGGGAAACACCTGCTTCATGAACTC
AGCTATTCAGTGTTTGAGCAACACACCTCCACTTACTGAATATTTCCTCAATGATAAGTATCAAGAAGAACTGAATTTTG
ACAATCCCTTAGGAATGAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCAAACAAATGTGGTCTGGAAAATTTAGC
TACATCGCACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGCACCGCAGTTCTCTGGATACCAGCAGCAAGACTGTCA
AGAATTACTAGCTTTCCTGTTGGATGGTCTACATGAGGATTTGAATAGAATTAGGAAAAAACCATACATACAACTAAAAT
ACGCCGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGCCTGGGAGAATCATTTAAAAAGAAATGATTCTATCATAGTC
GACATATTTCATGGCCTTTTCAAGTCAACTTTAGTATGTCCTGAATGTGCAAAGATTTCAGTCACATTTGACCCTTTTTG
TTACTTGACACTTCCTTTGCCCATGAAGAGCGTACCTTAGAAGTTTACTTAGTTAGAATGGATCCACTTACCAAACCTAT
GCAGTAGAAAGTGGTTGTCCCCAAAATTGGAAACATACAAGATCTTTGTACGGCCCTCTCTACTTTGTCAGGCGTACCTG
CAGATAAGATGATAGTCACTGATATATACAATTATAGATTTCACAGAATATTTGCCATGGATGAAAACCTTAGTAGTATT
ATGGAGCGAGATGATATTTATGTGTTTGAGATTAACATCAATAGGACAGAAGATACAGAGCATGTGATTATTCCTGTTTG
CCTAAGAGAAAAATTTAGACATTCAAGTTACACCCACCATACTGGTTCCTCACTTTTTGGTCAGCCTTTTCTTATAGCAG
TACCACGAAACAATACTGAAGATAAACTCTATAATCTTCTACTTTTGAGAATGTGCCGGTATGTCAAAATATCCACTGAA
ACTGAAGAAACTGAAGGATCCCTACATTGCTGTAAGGACCAAAATATTAATGGGAATGGCCCCAATGGCATCCATGAAGA
AGGCTCCCCAAGTGAAATGGAAACAGATGAGCCTGATGATGAGTCCAGCCAAGATCAAGAACTTCCCTCTGAGAATGAAA
CAGTCAGTCTGAGATTCAGTTGGAGGAGATAATGATTCTGAAAATGATTATGTACTGAGGAA

Alignment

ORF - retro_sara_230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.46 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STIQDAGLYQGQVLVIEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCL
          .TIQDAGLYQGQVL.IEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCL
Retrocopy ATIQDAGLYQGQVLAIEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCL

Parental  PSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMR
          PSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMR
Retrocopy PSYTAYKNYDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMR

Parental  GEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYI
          GEIAKSYAELIKQMWSGKFSY..PRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYI
Retrocopy GEIAKSYAELIKQMWSGKFSYIAPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYI

Parental  QLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFD-PFCYLTLPLPMKKER
          QLK.ADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFD.PF..L........ER
Retrocopy QLKYADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFD<PFLLLDTSFA-HEER

Parental  TLEVYLVRMDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIM
          TLEVYLVRMDPLTKPMQ.KVVVPKIGNIQDLCTAL.TLSGVPADKMIVTDIYN.RFHRIFAMDENLSSIM
Retrocopy TLEVYLVRMDPLTKPMQ*KVVVPKIGNIQDLCTALSTLSGVPADKMIVTDIYNYRFHRIFAMDENLSSIM

Parental  ERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRM
          ERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRM
Retrocopy ERDDIYVFEININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRM

Parental  CRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENE-NSQSE-D
          CRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENE.NSQSE.D
Retrocopy CRYVKISTETEETEGSLHCCKDQNINGNGPNGIHEEGSPSEMETDEPDDESSQDQELPSENE<NSQSE<D

Parental  SVGGDNDSENG-LCTEE
          SVGGDNDSEN..LCTEE
Retrocopy SVGGDNDSEND<LCTEE

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_230 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,