RetrogeneDB ID: retro_sara_189

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_6401:82736..83861(-)
• 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_189
ATGTTGGGACCTGTGCAAAGTAGGGCCAGAGTTTATGCGAATGTTAATACACAACGACCACGAGAATACTGGGATTACGA
GTCACTTGTGGTGGAATGGGGAAATCAAGATGACTATCAGCTAATGGGAAAATTAGGCCAGGGGAAATATAGTGAAGTAT
TTGAAGCCATCAAGAAATCAAATAATGAAAAAGTTGTTGTTAAAGTTCTCAAGCCAGTAAATGAGAAGAAAATCAAGCGT
GAAATAAAGATTTTGAAAAATTTGCAAGGTGGCCCAAACATCATCACATTGGTAGAAATTGTAAAAGATCCTCAGTCAAC
AAACCCCGCCATAGTTTTGGAACACGTAAACAGTACGGACTACAATCAACTGTACCCATTAACAGACCATGATATTCGGT
TTTATATCTATGAGATTTTGAAGGCCTTGGATTATAGTCACAGCATGGGCATTATGCATAGAGATGTGAAACCCCATAAT
GTTATGATTGATCATAAACACAGAAAGCTACGACTGATAGACTGGGGATTGGCTGAATTTTATCATCCCGGCCAACAATA
TAATGTCCAGGTTGCTTCCCGATACTTCAAAAGCCCTGAGCTCCTTCTAAACTACCAGATGTATGATTATAGCTTGGATA
TGTGGAGCTTGGGCTGTATGCTGGCAAGTATGATTTTTCTCAAGGAACCATTTTTCCATGGAGTTGATAATTATGATCAA
TTGTTGAGGATAGCCAGAGTTCTAGGGACAAAAGATTTATATGACTATATTCGTAAATACGGCATTAAATTAGACCGATG
TTTAAATGTAATTTTGGGCACACACTCACGTAAGACATGGGAGTGCTTTGTAAACAAAAATAACCAACACCTTGTCAACC
CAGAGGCCTTAAATTTACTGGACAAGCTTCTGAGATATGACCATCAGTCAAGGCTCACCGCCAGAGAGGCCATGGAGCAC
CCTTATTTCTCTACTGTTGTGAAGAACCAGGCTCAAGTGGGTTCATCTAGCAAGTCAGAGGGCTGTACACCTGTCAACAG
GACCAATATGTCAGGGATTTCGTAAGTGCCAGTTCCTTTATCCCTTAGACCTTTGGATGGCTCATCAGCGGTCGCTGCTT
CCAAT

Alignment

ORF - retro_sara_189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 95.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
          M.GPV.SRARVY..VNT.RPREYWDYES.VVEWGNQDDYQL..KLG.GKYSEVFEAI...NNEKVVVK.L
Retrocopy MLGPVQSRARVYANVNTQRPREYWDYESLVVEWGNQDDYQLMGKLGQGKYSEVFEAIKKSNNEKVVVKVL

Parental  KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
          KPV..KKIKREIKIL.NL.GGPNIITL..IVKDP.S..PA.V.EHVN.TD..QLY..LTD.DIRFY.YEI
Retrocopy KPVNEKKIKREIKILKNLQGGPNIITLVEIVKDPQSTNPAIVLEHVNSTDYNQLYP-LTDHDIRFYIYEI

Parental  LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
          LKALDY.HSMGIMHRDVKPHNVMIDH.HRKLRLIDWGLAEFYHPGQ.YNV.VASRYFK.PELL..YQMYD
Retrocopy LKALDYSHSMGIMHRDVKPHNVMIDHKHRKLRLIDWGLAEFYHPGQQYNVQVASRYFKSPELLLNYQMYD

Parental  YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR
          YSLDMWSLGCMLASMIF.KEPFFHG.DNYDQL.RIA.VLGT.DLYDYI.KY.I.LD...N.ILG.HSRK.
Retrocopy YSLDMWSLGCMLASMIFLKEPFFHGVDNYDQLLRIARVLGTKDLYDYIRKYGIKLDRCLNVILGTHSRKT

Parental  WERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMAGGSTPVSSAN
          WE.FV...NQHLV.PEAL..LDKLLRYDHQSRLTAREAMEHPYF.TVVK.QA..GSSS...G.TPV...N
Retrocopy WECFVNKNNQHLVNPEALNLLDKLLRYDHQSRLTAREAMEHPYFSTVVKNQAQVGSSSKSEGCTPVNRTN

Parental  MMSGISSVPTPSPLGPLAGSPVIAAAN
          .MSGIS.VP.P..L.PL.GS...AA.N
Retrocopy -MSGIS*VPVPLSLRPLDGSSAVAASN

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_189 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,