RetrogeneDB ID: retro_sara_534

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_231517:13441..14575(-)
• 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_534
TTGTCCCCACCCTTGCCAAGTAGGGCTAGAGTTTATGCAGATGTTAATACACGTCAACCCCCAGAATTTTGGGATCATGA
GTCATATGTGGTGAAATGGGGAAATATACGTGACTACAAAATAGGTAAAGTAATAGGTCGAGGGGGCTATAGCGAAGTAT
TTGAAGCTGTTAAAATTTTAACGAGTGAAAAGGTTGCTATTAAAGTACTCAGACCAACTAAGGAGGAGAAAATTAAGCGT
GAAATAAAGATTTTGGAGATGTTGCGAGGTGGTCCCAACATCATAAATTTGTTAGCAGTTGTCAAAATCCGTGATTCAGA
AGCCTTGGCCTTGGTTTTTGAATTCATAAACAACATTCAATTTAAGGAATTGCACCAGATATTAACAGACTATGAAATAC
GGTTTTACACCTATCAGATTCTGAAAGCTTTGGATTACTGTCATAGCATGGGAATTATGCACCGAGATCTCAAACCCGAA
AATATCATGATTGATCACAAACAAAGAAAGCTATGGTTGATCGACTGGGGAATGTCACAGTTTTATAATCCTGGTGAAGA
GTATAGTGCTGAAGTTGTTACCCGATTCTACAAAGGTCCTGAACTTCTGGTGGAGTATGAGATGTATGATTATAGTTTGG
ATATGTGGAGCTTGGGGTGTGTCCTGGCAAGCATGATCTTTCGCAAGGATCCATTTTTTGCGGGTAGCAATAATAATGAT
CAGTTGCTGAAGATAGTTAGCATTCTAGGAACAAACCGTTTTTATGCATACATTCAAAAATACAGAATCAAGTTAGATAA
ACAACTCCGAATAATCGTGGGCAAGCATCCTCGTGTTCGTTGGCAGCACTTCATCTCCGGTGAAAACAAGCACCTTGTCA
GCCCAGAAGCCCTTGATTTACTGGATAATCTGCTACAATATGACCCTCAGTTAAGGCTTACTGCGAGAGAGGCCATGGCA
CACCCCTATTTGTCCCCTTTTGTGAAGGAGCTTTCTCAAAGTCTTGGCGAGTCTAGCAGGTCAGCAGGAGGCAATATACC
TGCAACCAGTGACAGCACTATGCCAGGGACTTCTTCAGCACTAATGCCTTCGCTTCCTGGACAAAGGGCTGGTTTACCAG
TGGTTGGTGCTTCC

Alignment

ORF - retro_sara_534 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.64 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
          .S.P.PSRARVY.DVNT..P.E.WD.ES.VV.WGN..DY......GRG.YSEVFEA..I...EKV..K.L
Retrocopy LSPPLPSRARVYADVNTRQPPEFWDHESYVVKWGNIRDYKIGKVIGRGGYSEVFEAVKILTSEKVAIKVL

Parental  KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
          .P.K..KIKREIKILE.LRGGPNII.L...VK...S...ALVFE..NN..FK.L.Q.LTDY.IRFY.Y.I
Retrocopy RPTKEEKIKREIKILEMLRGGPNIINLLAVVKIRDSEALALVFEFINNIQFKELHQILTDYEIRFYTYQI

Parental  LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
          LKALDYCHSMGIMHRD.KP.N.MIDH..RKL.LIDWG...FY.PG.EY...V..R..KGPELLV.Y.MYD
Retrocopy LKALDYCHSMGIMHRDLKPENIMIDHKQRKLWLIDWGMSQFYNPGEEYSAEVVTRFYKGPELLVEYEMYD

Parental  YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR
          YSLDMWSLGC.LASMIFRK.PFF.G..N.DQL..I...LGT...Y.YI.KY.I.LD.....I.G.H.R.R
Retrocopy YSLDMWSLGCVLASMIFRKDPFFAGSNNNDQLLKIVSILGTNRFYAYIQKYRIKLDKQLRIIVGKHPRVR

Parental  WERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKD--QARMGSSSMAGGSTPVSS
          W..F...EN.HLVSPEALD.LD.LL.YD.Q.RLTAREAM.HPY....VK...Q....SS..AGG..P..S
Retrocopy WQHFISGENKHLVSPEALDLLDNLLQYDPQLRLTAREAMAHPYLSPFVKELSQSLGESSRSAGGNIPATS

Parental  ANMMSGISSVPTPSPLGPLAGSPVIAAA
          ...M.G.SS...PS..G..AG.PV..A.
Retrocopy DSTMPGTSSALMPSLPGQRAGLPVVGAS

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_534 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.

---

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,