RetrogeneDB ID: retro_sara_303

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_154819:2..1521(-)
• 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_303
AAAGTAGAAGTATATGAAAATGGCAACCTGAATAATGTTGTAACAAAAGATTTAGCAAAGCTAACACAATAGGTACAATT
GAAAAGGAAATCAGAAAAATCTTCAATATTCCAGATGAGAAGGAGACGAGATTGTGGAACAAATACATGAGTAATACATT
TGAGCCACTGAATAAACCGGACAGCACTATTCAGGATGCTGGTTTATACCAAGGACAGGTGTTAGTGATAGAACAGAAAA
ATGAAGATGGAACATGGCCAAGGGGTCCTTCTGCTCCTAAGTCCGCAGGTGCATCCAATTTTTCAACTTTACCAAAGATA
TCTCCTTCATCTCTATCAAATAATTATAACAACATCAACAACAGAAATGTGAGAAACTCAAATTATTGTCTTCCATCATA
TACTGCTTATAAGAAATATGATTATTCAGAACCTGGAAGAAATAATGAGCAGCCAGGCCTCTGTGGCCTGAGTAACTTGG
GAAACACCTGCTTCATGAACTCAGCTATTCAGTGTTTGAGCAACACACCTCCACTTACTGAATATTTCCTCAATGATAAG
TACCAAGAAGAACTGAATTTTGACAATCCCTTAGGTATGAGAGGTGAAATAGCTAAGTCTTATGCTGAATTGATCAAACA
AATGTGGTCTGGAAAATTTAGGTACGTCACACCAAGAGCCTTTAAGACACAAGTAGGACGTTTTGTACCACAGTTCTCTG
GATACCAGCAGCAAGACTGTCAAGAATTACTAGCTTTCCTGTTGGATGGTCTACATGAGGATTTGAATAGAATTAGGAAA
AAACCATACATACAATTAAAAGACGCCGATGGGAGGCCAGATAAGGTGGTTGCTGAAGAAGCCTGGGAAAATCATTTAAA
AAGAAATGATTCTATCATAGTCGACATATTTCATGGCCTTTTCAAGTCAACTTAGGATGTCCTGAATGTGCAAAGATTTC
AGTCACATTTGATCCTTTTTGTTACTTGACACTTCCTTTGCCCATGAAAAAAGAGCATACCTTAGAAGTTTACTTAGTTA
GAATGGATCCACTTACCAAACCTATGCAGTACAAAGGGGTTGTTCCCAAAATTGGAAACATACAAGATCTTTGTACGGCA
CTCTCTACTTTGTCAGGCATACCTGCAGATAAGATAATAGTCACTGATATATACAATCATAGATTTCACAGAATATTTGC
CATGGATGAAAACCTTAGTAGTATTATGGATCGAGATGATATTTATGTGTTTGAGATTAACATCAAGAGGACAGAAGATA
CAGAGCATGTGATTATTCCTGTTTGCCTAAGAGAAAAATTTAGACATTCAAGTTACACGCACCAAACTGGTTCCTCACTT
TTTGGTCAGCCTTTTGTTTTAGCAGTACCACGAAACAATACTGAAGATAAACTCTATAATCTTCTACTTTTAAGAATGTG
CCGGTATGTCAAAATATCCACTGAAACTGAAGAAACTGAAGGATCCCTACATTGCTGTAAGGACCAAAATATTAATGGG

Alignment

ORF - retro_sara_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.7 %
• Parental protein coverage: 51.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELKLCENGNMNNVVTR-RFSKADTIDTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGL
          .....ENGN.NNVVT..RFSKA.TI.TIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGL
Retrocopy KVEVYENGNLNNVVTK<RFSKANTIGTIEKEIRKIFNIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGL

Parental  YQGQVLVIEQKNEDGTWPRGPSAPKSPGASNFSTLPKISPSSLSNNYNNINNRNVKNSNYCLPSYTAYKN
          YQGQVLVIEQKNEDGTWPRGPSAPKS.GASNFSTLPKISPSSLSNNYNNINNRNV.NSNYCLPSYTAYK.
Retrocopy YQGQVLVIEQKNEDGTWPRGPSAPKSAGASNFSTLPKISPSSLSNNYNNINNRNVRNSNYCLPSYTAYKK

Parental  YDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYA
          YDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYA
Retrocopy YDYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYA

Parental  ELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGR
          ELIKQMWSGKF.YVTPRAFKTQVGRF.PQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGR
Retrocopy ELIKQMWSGKFRYVTPRAFKTQVGRFVPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGR

Parental  PDKVVAEEAWENHLKRNDSIIVDIFHGLFKST-LVCPECAKISVTFDPFCYLTLPLPMKKERTLEVYLVR
          PDKVVAEEAWENHLKRNDSIIVDIFHGLFKST.L.CPECAKISVTFDPFCYLTLPLPMKKE.TLEVYLVR
Retrocopy PDKVVAEEAWENHLKRNDSIIVDIFHGLFKST<LGCPECAKISVTFDPFCYLTLPLPMKKEHTLEVYLVR

Parental  MDPLTKPMQYKVVVPKIGNIQDLCTALCTLSGVPADKMIVTDIYNHRFHRIFAMDENLSSIMERDDIYVF
          MDPLTKPMQYK.VVPKIGNIQDLCTAL.TLSG.PADK.IVTDIYNHRFHRIFAMDENLSSIM.RDDIYVF
Retrocopy MDPLTKPMQYKGVVPKIGNIQDLCTALSTLSGIPADKIIVTDIYNHRFHRIFAMDENLSSIMDRDDIYVF

Parental  EININRTEDTEHVIIPVCLREKFRHSSYTHHTGSSLFGQPFLIAVPRNNTEDKLYNLLLLRMCRYVKIST
          EINI.RTEDTEHVIIPVCLREKFRHSSYTH.TGSSLFGQPF..AVPRNNTEDKLYNLLLLRMCRYVKIST
Retrocopy EINIKRTEDTEHVIIPVCLREKFRHSSYTHQTGSSLFGQPFVLAVPRNNTEDKLYNLLLLRMCRYVKIST

Parental  ETEETEGSLHCCKDQNING
          ETEETEGSLHCCKDQNING
Retrocopy ETEETEGSLHCCKDQNING

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_303 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,