RetrogeneDB ID: retro_sara_468

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_218821:896..2025(-)
• 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_468
ATGTCGATATCCAAACAAAGTAGGGCAAGAGTTTATGCAGAGGTTAATGCAGAACGACCCAGAGAATACTGGGATTATGA
ATCATATGTGGTGGAGTGGGGAAAACGTGATGATTACCATCTCATTCGAAAACTGGGCAAGGGAAACTATAGTGAAGTAT
TTGAAGCTATCAACACTAAAAATAGGAAAAAAGTTGCCATTAAAATACTCAAGCCAGTAACGGATAATAAAGTCAAGCGT
GAAATAAAGATTTTGGAGAATTTGCGTGGTGGTCCCAACATCATATATTTACAAGACATTATAAAATGCCCTAGTATAGG
AGCACCTGCCTTGGTGTTTGAGCTTGTAAACAACAGAGATTACAAAGAATTGTACCATACATTCACTGACTATGATATTC
GGTTCTACATCTATGAGATTTTGAAGGCCTTGGACTATAGTCATAGCATGGGGATTATGCACAGAGATCTGAAACCCCAT
AATGTTATGATTGACCATGAAAACAGAAAGCTATGGCTAATTGACTGGGGGTTGGCTGATTTTTTCCATCCTGGAAGAGA
ATATAATGTTCGAGTTGCATCCCGATACTTTAAAGGTCCTGAGCTAATTGTAGAATATGAGATGTATGATTATAGTCTAG
ATTTATGGAGCTTGGGTTGCATGCTGGCAAGTATGATATTTCGCAAGGAGCCATTTTTTCATGGTAATGATAATGATGAT
CAGTTGTTGAAAATAGCCAACGTTCTGGGCACGAAAGATTTCTATAATTATATTAACAAATACAAAATCTTATTAGATTC
CCCATTTCAAAGTAATGTTAGGCACACAACCCCGAAAGCATTGGGGTTGCTTTGTTCACAGTGAGAACCAGCACCTTGTC
AGCCCAGAAGCCTTTGATATTCTAGACAAGCTGCTAGTATATGACCATCAGTCACGGCTCACTGCCAGAGAGGCCATGGA
ACACCCATATTTTTGTACTGTAGTTAAGAACCAAACTCAACTTGATTCATGTAGTAAACCAGGACAGAAAATGCATGAAG
AAAGGGGCAGTATGAATCCAGGTAATTCTTTAGGGCCAGGATCTTCAGCCCTTGGACGTCAGGCAGATCCACCGGTGACA
GGTGCTGCT

Alignment

ORF - retro_sara_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
          MS....SRARVY..VN..RPREYWDYES.VVEWG..DDY.L.RKLG.G.YSEVFEAIN..N..KV..KIL
Retrocopy MSISKQSRARVYAEVNAERPREYWDYESYVVEWGKRDDYHLIRKLGKGNYSEVFEAINTKNRKKVAIKIL

Parental  KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
          KPV...K.KREIKILENLRGGPNII.L.DI.K.P....PALVFE.VNN.D.K.LY.T.TDYDIRFY.YEI
Retrocopy KPVTDNKVKREIKILENLRGGPNIIYLQDIIKCPSIGAPALVFELVNNRDYKELYHTFTDYDIRFYIYEI

Parental  LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
          LKALDY.HSMGIMHRD.KPHNVMIDHE.RKL.LIDWGLA.F.HPG.EYNVRVASRYFKGPEL.V.Y.MYD
Retrocopy LKALDYSHSMGIMHRDLKPHNVMIDHENRKLWLIDWGLADFFHPGREYNVRVASRYFKGPELIVEYEMYD

Parental  YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELD-PRFNDILGRHSRK
          YSLD.WSLGCMLASMIFRKEPFFHG.DN.DQL..IA.VLGT.D.Y.YI.KY.I.LD.P.F...LG...RK
Retrocopy YSLDLWSLGCMLASMIFRKEPFFHGNDNDDQLLKIANVLGTKDFYNYINKYKILLD>PHFKVMLGTQPRK

Parental  RWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMAGGSTPVSSA
          .W..FVHSENQHLVSPEA.D.LDKLL.YDHQSRLTAREAMEHPYF.TVVK.Q....S.S..G........
Retrocopy HWGCFVHSENQHLVSPEAFDILDKLLVYDHQSRLTAREAMEHPYFCTVVKNQTQLDSCSKPGQKMHEERG

Parental  NMMSGISSVPTPSPLGPLAGSPVIAAA
          .M..G.S..P..S.LG..A..PV..AA
Retrocopy SMNPGNSLGPGSSALGRQADPPVTGAA

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_468 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,