RetrogeneDB ID: retro_sara_357

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_178361:16439..17421(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2A3
• Ensembl ID: ENSSARG00000002896
• Aliases: None
• Description: casein kinase 2, alpha 3 polypeptide [Source:HGNC Symbol;Acc:2458]

Sequence

>retro_sara_357
CCCTTGCCAAGCAGGGCTAGAGTGTATGCAGATGTAAACTCACACCGACCTACACGTTATTGGGATTTTGAGTCACATGA
GGAGGAATGGGGAAATCTTGATGACTACAAGCTGGGCCAACTAATAGGACGGGGAAACTATAGTGATGTATTTGAGGCAT
ACAAAAAGAAATCAAATAAAAAAACTGCAGTGAAAATACTCTACTCAGTCAATTATATAAAAATCAAACGTGAAATCACA
ATTTTGGAGAACTTAAGAGGTGGTCCCAACATCGTAACACTGATAGACACTGTAAGAAACGTTGATTCAGGAGACATTGC
ATTAGTATTTGAGTTTCTAAAAAACACCAATTATAAGAAATTGTACCCGACCTTAACAGACTATGATATACGGTTTTACA
CCTATGAGATACTGAAGGCTTTGGATTATGCTCATAGCATGGGAATTATGCACCGAGATCTCAAACCTGAAAATATCTTG
ATTGATCACAAGAAAAGAACCATACGGCTCATCGACTGGGGCTTGTCAGACTTTTATCATCCTGGTTTTCATGTATAATG
TTCATGTTGCTTCACTGCACTATAAGGGACCAGAGCTATTGGTTAATTATGAGATGTATGATTATAGCTTGGATAATGTG
GAGCCTGGGGTGTGTCCTAGCATGCATGGTCTTTCATAAGGAACCATTTTTCCCTGGTAACGATCATTTTGATCAGTTGG
TGAGGATAATAAATGTTCTGGGAACAGACGAATTTTATAAATACATTGAAAAATACAAGATCACTTTAGAGTCACGTACC
AAAGCACTCTTAACCACACAACCCCGCCAGGAATGGGAGTGTTTCGTGCACAGTGAGAACCAGCACCTTGTAAGCCCAGA
AGCCTTTTGATATCTTAGATAAAGCTGCTAAATTATGCCCTCAAGTCACGGCTTCCTGCTCAGAGGGTTATGAAACATTC
TTATTTCTCAGTTCTCATGAAG

Alignment

ORF - retro_sara_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.94 %
• Parental protein coverage: 82.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPV
          P.PSRARVY.DVN.HRP..YWD.ESH..EWGN.DDY.L....GRG.YS.VFEA..........VKIL..V
Retrocopy PLPSRARVYADVNSHRPTRYWDFESHEEEWGNLDDYKLGQLIGRGNYSDVFEAXXXXXXXXXAVKILYSV

Parental  KKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKA
          ...KIKREI.ILENLRGGPNI.TL.D.V....S...ALVFE...NT..K.LY.TLTDYDIRFY.YEILKA
Retrocopy NYIKIKREITILENLRGGPNIVTLIDTVRNVDSGDIALVFEFLKNTNYKKLYPTLTDYDIRFYTYEILKA

Parental  LDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQE-YNVRVASRYFKGPELLVDYQMYDYS
          LDY.HSMGIMHRD.KP.N..IDH..R..RLIDWGL..FYHPG...YNV.VAS...KGPELLV.Y.MYDYS
Retrocopy LDYAHSMGIMHRDLKPENILIDHKKRTIRLIDWGLSDFYHPGFH>YNVHVASLHYKGPELLVNYEMYDYS

Parental  LD-MWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRW
          LD.MWSLGC.LA.M.F.KEPFF.G.D..DQLVRI..VLGT...Y.YI.KY.I.L..R....L....R..W
Retrocopy LD>MWSLGCVLACMVFHKEPFFPGNDHFDQLVRIINVLGTDEFYKYIEKYKITLESRTKALLTTQPRQEW

Parental  ERFVHSENQHLVSPEA-LDFLD-KLLRYDHQSRLTAREAMEHPYFYTVVK
          E.FVHSENQHLVSPEA..D.LD.KLL.Y...SRL.A...M.H.YF....K
Retrocopy ECFVHSENQHLVSPEA>FDILD>KLLNYALKSRLPAQRVMKHSYFSVLMK

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_357 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 4 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014039	2 retrocopies	retro_amel_138, retro_amel_1888,
Homo sapiens	ENSG00000101266	1 retrocopy	retro_hsap_53,
Sorex araneus	ENSSARG00000002896	10 retrocopies	retro_sara_188, retro_sara_189, retro_sara_240, retro_sara_357 , retro_sara_468, retro_sara_508, retro_sara_534, retro_sara_572, retro_sara_738, retro_sara_755,
Tursiops truncatus	ENSTTRG00000007064	1 retrocopy	retro_ttru_1605,