RetrogeneDB ID: retro_sara_572

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_234967:39198..40275(-)
• 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_572
CCCTTACCAAGCAGGGCTAGAGTTTATGCAGATGTTAATGCAGAACGACCCAAAGAATACTGGGATTATGCATCCCATGT
GGAAGTATGGGGAAATCTAGATGATTATAAATTGGGTAAAAAAATAGGCCATGGAAGCTCATGTGATGTATTTGAAGCTG
TCAAAATTGCAACGAATGAAAAAGTTGCTATTAAAGTACTCAAAGGAATTGCAGAGGTGAAAATTAAGCGAGAAATAACA
GTTCTGGAGAATTTACGCGGAGGCCCCAACATCATAACTTTGCTAGCCACTGTAAAACGTCCTGAGTCAGAAACAACAGC
CTTAGTTTTTGAATATGTAAACAATACCCATTACAAGAAATTATACCGTACCTTAACAGACTTTGAAATACGGTTTTATA
CCTATGAGCTGCTGAAGGCTTTAGATTACAGTCATAGCATGGGAATTATGCACCGAGATCTCAAACCCGAAAACATCATG
ATAGATCAAGAGAACAGAAAGCTATGGCTAATTGACTGGGGGTTGGCAGAATTTTATCATCCTGGCAAAGAATACAATAC
ACGAATTGCTTCCCGATGCTTCAAAGCTCCTGAGCTGCTGATTGAATATGACACTTATGATTATAGTATGGATATGTGGA
GCCTAGGATGTATCCTGGCAAGCCTGGTCTTTCAGAAAGAACCATTTTTTTATGGTCGTGATAACAAAGATCAATTGCTG
AAGATAGTCAACATTATGGGAACAGAGCATTTTTTTGAGTACATTGAAAACCAGAATATCTACTTAGATCCACGTCTCCG
TGTATTCTTGGGCACGCACCTCCGTGTTCGATGGGAGCGCTTTATCCACACTGGCAACCAGCACCTTGTCAACCCACTAG
CTTTTGATATTCTAGATAAGCTGTTACAATTTGACCCTCATTTAAGGCTTACTGCCAGAGAGGCCATGGAGCACCCTTAT
TTCAAAATTGTTGTGGGGCGCAAGGGTCTGGTATCTCAGAACTCTAGCAGTACTTCTTCCACCAGTGATAGCAGTGTGCC
AGGGACTTCTTCAGCATCAGAGCCTCCACCCCCTACA

Alignment

ORF - retro_sara_572 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.23 %
• Parental protein coverage: 90.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPV
          P.PSRARVY.DVN..RP.EYWDY.SHV..WGN.DDY.L..K.G.G....VFEA..I..NEKV..K.LK..
Retrocopy PLPSRARVYADVNAERPKEYWDYASHVEVWGNLDDYKLGKKIGHGSSCDVFEAVKIATNEKVAIKVLKGI

Parental  KKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKA
          ...KIKREI..LENLRGGPNIITL...VK.P.S.T.ALVFE.VNNT..K.LY.TLTD..IRFY.YE.LKA
Retrocopy AEVKIKREITVLENLRGGPNIITLLATVKRPESETTALVFEYVNNTHYKKLYRTLTDFEIRFYTYELLKA

Parental  LDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSL
          LDY.HSMGIMHRD.KP.N.MID.E.RKL.LIDWGLAEFYHPG.EYN.R.ASR.FK.PELL..Y..YDYS.
Retrocopy LDYSHSMGIMHRDLKPENIMIDQENRKLWLIDWGLAEFYHPGKEYNTRIASRCFKAPELLIEYDTYDYSM

Parental  DMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWER
          DMWSLGC.LAS..F.KEPFF.G.DN.DQL..I....GTE....YI...NI.LDPR....LG.H.R.RWER
Retrocopy DMWSLGCILASLVFQKEPFFYGRDNKDQLLKIVNIMGTEHFFEYIENQNIYLDPRLRVFLGTHLRVRWER

Parental  FVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMAGGSTPVSSANMMS
          F.H..NQHLV.P.A.D.LDKLL..D...RLTAREAMEHPYF..VV.........S....ST..SS....S
Retrocopy FIHTGNQHLVNPLAFDILDKLLQFDPHLRLTAREAMEHPYFKIVVGRKGLVSQNSSSTSSTSDSSVPGTS

Parental  GISSVPTPS
          ..S..P.P.
Retrocopy SASEPPPPT

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_572 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,