RetrogeneDB ID: retro_sara_550

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_232905:37674..39690(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: USP4
• Ensembl ID: ENSSARG00000007703
• Aliases: None
• Description: ubiquitin specific peptidase 4 (proto-oncogene) [Source:HGNC Symbol;Acc:12627]

Sequence

>retro_sara_550
GAACACAACCTGTTTCCTGGCCCAATAGATAACTCTGGACTCTTTTCAGATCCAGAGAGTCAGACCCTGAAAGAACATTT
AATTCATGAATTGGATTATGTATTGGTTCCAACTGAGGCCTGGAACAAGTTGTTAAACTGGTATGGTTGTGTTGAAGGGC
AGCAGCCCATTGTGCGAAAGGTTGTAGAGCATGGCCTGTTTGTCAAACACTGCAAAGTAGAAGTGTACTTGCTGGAACTG
AAGCTCTGTGAGAATAGTAACCCCACCAATGTTCTGAGTTGCCATTTCAGCAAGGCAGATACCATTGCAACCATTGAGAA
GGAGATGTGGAAACTGTTCAACATTCCTTCAGAACGTGAAACAAGACTGTGGAACAAATACATGAGCAATACCTATGAGC
AGCTGAGCAAGCTCGATAACACTGTTCAGGATGCGGGGCTTTACCAGGGCCAGGTGCTGGTAATTGAGCCTCAGAATGAA
GATGGTACATGGCCGAGGCAGACCCTTCAGACAAAATCAAGCACTGCGCCTAGCAGAAATTTCACTACCTCTCCCAAATC
GTCAGCGAGCCCCTACGCCTCAGTGGCTGCCTCTACCATTGCATATGGTGATAGCACTAACACCTCTGGGGTGCACAGTT
CCAGTGTCAGCCGGGGTGGCTCTGGCTTCTCTGCTTCATATAATTGTCAGGAGGCCTCCTCATCTCAAGTACAACCTGGG
ATCTATGGACTCGGAAACCTGGGGAACACCTGCTTCATGAACTCGGCTTTGCAGTGCTTGAGCAACACCGCGCCACTAAC
GGACTACTTCCTTGACGATGAATATGAAGCGGAGATCAATAGAGACAACTCGCTGGGGATGAAAGGGGAAATCACAGAGG
CCTATGCAGAGCTCATTAAGCAGATGTGGTCTGGCAGGGATGCCCATGTGGCACCACGTATGTTCAAAACACAAGTGGGA
CGTTTTGCCCCCCAGTTTTCTGGCTACCAGCAGCAAGACTCTCAAGAGCTGTTAGCCTTTCTTCTGGATGGATTGCATGA
AGATCTGAACCGAGTGAAGAAGAAGCCCTACCTGGAGCTGAAGGACGCCAATGGGCGGCCAGATGCGGTGGTAGCAAAGG
AAGCCTGGGAGAACCACAGGTTAAGGAATGATTCTGTGATTGTGGATACATTCCATGGCCTCTTCAAGACTACTTTGGTT
TGCCCTGAGTGTGCAAAGGTTTCAGTGACCTTTGACCCATTTTGCTATCTCACTCTCCCACTGCCCTTGAAGAAAGATCG
GGTTATGGAGGTCTTCCTGGTTCCTGCTGACCCTCGCTGCAGACCTACTCAGTACTGCGTGATTGTGCCACTGATGGGGA
CCGTGTCCAATCTCTGCGAGGTGCTCTCCAGGCTGTCTGGCATTGCTGCAGAAAATATGGTGGTCACTGATGTGTATAAC
CATCGATTCCACAAAATTTTCCAAATGGATGAAGGTTTGAACCACATCATGCCTCGGGATGACATCTTTGTGTATGAAGT
CTGCAGCACTTCCACTGATGGTACAGAGTACATCACACTTCCAGTCTACTTCAGGGAGAGGAAGTCCAGGACTCCGAGTA
CATCCTCGGTAGCAGTGCTTTATGGACAGCCACTGCTGGTTTTCGTCCCCAAGCACAAGCTAACCCTCGATTCTTTGTAC
CAGGCTGTCTGTGAGTGTATCAGCCGCTATATAAAATAGCCTTTGCCCGATGAGTCTGGCAGCTCGCCCTTGGAGCCCGG
GTCCTACATTGGCTCCAGGAGCAGCTGTGAAGGAGAAGATGAAGAAGAAATGCAGCATCAGGAAGAAGGTAAAGAGCAGC
TGTCTGAGATGGAAGGCAGTGGCGAGGAGGAGCTGGAAAATGACCAGGGTGAGACTACCCAGAAGGTCCGAGACCAGCAC
TGTCCCAGGAGGCTTTTTACCTTCAGCCTTGTGAACTCCTATGGAACAGCTGACATCAATTCACTGGCAATAGATGGAAA
ACTACATAAACTCAAC

Alignment

ORF - retro_sara_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 69.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EHNLFPGPIDNSGLFSDPESQTLKEHLIDELDYVLVPTEAWNKLLNWYGCVEGQQPIVRKVVEHGLFVKH
          EHNLFPGPIDNSGLFSDPESQTLKEHLI.ELDYVLVPTEAWNKLLNWYGCVEGQQPIVRKVVEHGLFVKH
Retrocopy EHNLFPGPIDNSGLFSDPESQTLKEHLIHELDYVLVPTEAWNKLLNWYGCVEGQQPIVRKVVEHGLFVKH

Parental  CKVEVYLLELKLCENSDPTNVLSCHFSKADTIATIEREMRKLFNIPAERETRLWNKYMSNTYEQLSKLDN
          CKVEVYLLELKLCENS.PTNVLSCHFSKADTIATIE.EM.KLFNIP.ERETRLWNKYMSNTYEQLSKLDN
Retrocopy CKVEVYLLELKLCENSNPTNVLSCHFSKADTIATIEKEMWKLFNIPSERETRLWNKYMSNTYEQLSKLDN

Parental  TVQDAGLYQGQVLVIEPQNEDGTWPRQTLQTKSSTAPSRNFTTSPKSSASPYTSAAASPVANGDSTNTSG
          TVQDAGLYQGQVLVIEPQNEDGTWPRQTLQTKSSTAPSRNFTTSPKSSASPY.S.AAS..A.GDSTNTSG
Retrocopy TVQDAGLYQGQVLVIEPQNEDGTWPRQTLQTKSSTAPSRNFTTSPKSSASPYASVAASTIAYGDSTNTSG

Parental  VHSSSVSRGGSGFSASYNCQEASSSQVQPGICGLGNLGNTCFMNSALQCLSNTAPLTDYFLDDEYEAEIN
          VHSSSVSRGGSGFSASYNCQEASSSQVQPGI.GLGNLGNTCFMNSALQCLSNTAPLTDYFLDDEYEAEIN
Retrocopy VHSSSVSRGGSGFSASYNCQEASSSQVQPGIYGLGNLGNTCFMNSALQCLSNTAPLTDYFLDDEYEAEIN

Parental  RDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLN
          RDN.LGMKGEI.EAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLN
Retrocopy RDNSLGMKGEITEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLN

Parental  RVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLP
          RVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFK.TLVCPECAKVSVTFDPFCYLTLP
Retrocopy RVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKTTLVCPECAKVSVTFDPFCYLTLP

Parental  LPLKKDRVMEVFLVPADPRCRPTQYRVIVPLMGAVSDLCEALSRLSGIAAENMVVTDVYNHRFHKIFQMD
          LPLKKDRVMEVFLVPADPRCRPTQY.VIVPLMG.VS.LCE.LSRLSGIAAENMVVTDVYNHRFHKIFQMD
Retrocopy LPLKKDRVMEVFLVPADPRCRPTQYCVIVPLMGTVSNLCEVLSRLSGIAAENMVVTDVYNHRFHKIFQMD

Parental  EGLNHIMPRDDXXXYEVCSTSLMVPEYITLPIYFRERKSRPSSTSSVAVLYGQPLLVSVPKHKLTVDSLY
          EGLNHIMPRDD...YEVCSTS....EYITLP.YFRERKSR..STSSVAVLYGQPLLV.VPKHKLT.DSLY
Retrocopy EGLNHIMPRDDIFVYEVCSTSTDGTEYITLPVYFRERKSRTPSTSSVAVLYGQPLLVFVPKHKLTLDSLY

Parental  QAVCERIRRYKQ--LADESGSSPLKGSCNL--RASC--EDEEEMEHQEEGKEQLSETEGSGEEELGNDQG
          QAVCE.I.RY....L.DESGSSPL........R.SC..EDEEEM.HQEEGKEQLSE.EGSGEEEL.NDQG
Retrocopy QAVCECISRYIK*PLPDESGSSPLEPGSYIGSRSSCEGEDEEEMQHQEEGKEQLSEMEGSGEEELENDQG

Parental  ETTQKVRDQRCPRRLFTFSLVNSYGTADINSLATDGKLLKLN
          ETTQKVRDQ.CPRRLFTFSLVNSYGTADINSLA.DGKL.KLN
Retrocopy ETTQKVRDQHCPRRLFTFSLVNSYGTADINSLAIDGKLHKLN

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_550 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 3 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013001	1 retrocopy	retro_mdom_696,
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 ,