RetrogeneDB ID: retro_sara_508

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_229144:6532..7502(-)
• 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_508
GTGTCCCTACCCTTGTCAAGCAGGGCTAGAGTTTATGCAGATGTTAATGCACATCAACCCAGAAAATACTGGGATTATGA
GTCACATGTGGTGCACTGGGGGAATCTAGATGACTACGATCTGGGAAAAAGAATTGGCCACGGAAGCTATAGTGAAGTAT
TTGAAGCTGTCAAACTCTCAACAAATGAAAAGTTTGTTGTTAAACTCCTCAGCCCAATCCTAGAGGAGAAAGTCAAGCGT
GAAATAAAGATTTTGGAGAATTTGCGAGGTGGTCCTAACATCATAACTTTGACAGACGTTGTGAAAAATCATGAGTCAGG
AACCCCTGGCTTGGTTTTTGAATATATAAACAACACTCACCACAAGAAGTTGTACCAGAAATTAACAGACTATGATGTAC
GGTTTTACACCTATGAGACTCTGAAAGCTCTGGATTACTGTCATAGCATGGGAATTATGCACCGAGATCTCAAACCTGAA
AACATCATGATTGATCATGAGAAAAGAAAGCTATGGATAATTGACTGGGGATTGTCGGAATTTTACCATCCTGGTGAGGA
GTATAGTACTCAAGTTGTTACAAGATATTTCAAAGGCCCTGAGCTGCTGGTCGATTATGAGATGTATGATTATAGTTTGG
ACATGTGGAGCCTGGGGTGTATCCTGGCAAGCATGATCTTTCACAGGGAGCCGTTTTTTCGTGGTCGTGATGATAATGAT
CAGTTGGCGAAGATAGTCACCATTCTAGGAACAAGCCGTTTTTATGAGTACATTAAGAAATACAAGATAAAGATAGATAA
ACATCTTCAAGTAATCGTGGGCAAGCATTCCCGTATTCGTTGGCATCACTTTGTCCGCAATGAAAACGATCACCTTGTCA
GCCCAGAAGCCTTTGATTTTCCTGGATAGGGTGCTACAATATGACCCTCAGTTAAGGCTTACCGCCAGAGAAGCCATGGT
ACACCCCTAT

Alignment

ORF - retro_sara_508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 81.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
          .S.P..SRARVY.DVN.H.PR.YWDYESHVV.WGN.DDY.L....G.G.YSEVFEA.....NEK.VVK.L
Retrocopy VSLPLSSRARVYADVNAHQPRKYWDYESHVVHWGNLDDYDLGKRIGHGSYSEVFEAVKLSTNEKFVVKLL

Parental  KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
          .P....K.KREIKILENLRGGPNIITL.D.VK...S.TP.LVFE..NNT..K.LYQ.LTDYD.RFY.YE.
Retrocopy SPILEEKVKREIKILENLRGGPNIITLTDVVKNHESGTPGLVFEYINNTHHKKLYQKLTDYDVRFYTYET

Parental  LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
          LKALDYCHSMGIMHRD.KP.N.MIDHE.RKL..IDWGL.EFYHPG.EY...V..RYFKGPELLVDY.MYD
Retrocopy LKALDYCHSMGIMHRDLKPENIMIDHEKRKLWIIDWGLSEFYHPGEEYSTQVVTRYFKGPELLVDYEMYD

Parental  YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR
          YSLDMWSLGC.LASMIF..EPFF.G.D..DQL..I...LGT...Y.YI.KY.I..D.....I.G.HSR.R
Retrocopy YSLDMWSLGCILASMIFHREPFFRGRDDNDQLAKIVTILGTSRFYEYIKKYKIKIDKHLQVIVGKHSRIR

Parental  WERFVHSENQHLVSPEALD-FLDKLLRYDHQSRLTAREAMEHPY
          W..FV..EN.HLVSPEA.D.FLD..L.YD.Q.RLTAREAM.HPY
Retrocopy WHHFVRNENDHLVSPEAFD>FLDRVLQYDPQLRLTAREAMVHPY

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_508 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,