RetrogeneDB ID: retro_sara_240

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_128618:3..717(-)
• 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_240
ATGTCGGTACCCATGCCAAGCAGAGCAAGAGTATATGCAGAGGTTAATACACAACGACCCAAAGAGTACTGGGATTATGA
ATCATATGTGGTGGAGTGGGGAAAACGTGATGACTACCAGCTCATTCGAAAACTAGGCAGGGGAAACTATAGTGAAGTAT
TTGAAGCCATCAACATTAACAATAATAAAAAAGTTGCTGTTAAAATACTGAAGCCAGTAATGGAGAATAAAGTCAAGCGT
GAAATAAAGATTTTGGAGAATTTGCGAGCTGGCCCCAACATCATATATTTGACAGACATTATAAAAAGCCCTAATTTAGG
AGCCCCTGCCTTGGTGTTTGAGCACGTAAACAACAGAGACTACAGACAATTGTACAAGACATTAACTGACTATGATATCC
GTTTCTATATGTATGAGATTTTGAAGGCCTTGGACTACAGTCATAGCATGGGGATTATGCACAGAGATCTGAAACCCCAT
AACATTATGATTGACCATGAAAACAGAAAGTTACGGCTAATTGACTGGGGGTTAGCTGATTTTTACCATCCTGGAAAAGC
GTATAATGTTCGCGTTGCATCCCGGTTCTTCAAGGGTCCTGAGTTGCTAGTAGAGTATGAAATGTATGATTATAGTTTGG
ATTTATGGAGCTTGGGATGCATGCTGGCAAGTATGGTCTTTCGCAAGGAGCCATTTTTTCATGGTAACGATAAT

Alignment

ORF - retro_sara_240 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 60.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
          MS.P.PSRARVY..VNT.RP.EYWDYES.VVEWG..DDYQL.RKLGRG.YSEVFEAINI.NN.KV.VKIL
Retrocopy MSVPMPSRARVYAEVNTQRPKEYWDYESYVVEWGKRDDYQLIRKLGRGNYSEVFEAININNNKKVAVKIL

Parental  KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
          KPV...K.KREIKILENLR.GPNII.L.DI.K.P....PALVFEHVNN.D..QLY.TLTDYDIRFYMYEI
Retrocopy KPVMENKVKREIKILENLRAGPNIIYLTDIIKSPNLGAPALVFEHVNNRDYRQLYKTLTDYDIRFYMYEI

Parental  LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
          LKALDY.HSMGIMHRD.KPHN.MIDHE.RKLRLIDWGLA.FYHPG..YNVRVASR.FKGPELLV.Y.MYD
Retrocopy LKALDYSHSMGIMHRDLKPHNIMIDHENRKLRLIDWGLADFYHPGKAYNVRVASRFFKGPELLVEYEMYD

Parental  YSLDMWSLGCMLASMIFRKEPFFHGHDN
          YSLD.WSLGCMLASM.FRKEPFFHG.DN
Retrocopy YSLDLWSLGCMLASMVFRKEPFFHGNDN

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_240 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,