RetrogeneDB ID: retro_cfam_1408

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:26134656..26135453(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CSNK2A1
• Ensembl ID: ENSCAFG00000006946
• Aliases: None
• Description: casein kinase 2, alpha 1 polypeptide [Source:HGNC Symbol;Acc:2457]

Sequence

>retro_cfam_1408
CGCAAGCCAGTTAAAGGTGAAATAAAGATTTTGGAGAATTTATGAGGCAGTCCCAATATTATCACAATGGCAGATATTGT
TAAAGACCCTGTGTCATGAACTCTTGCCTTGGTTTTTGAACATATAAACAACACAGACTTTGAGCAATTGTACCGGATGT
TAACAGACTATGATATTCTATTTTACATGTATGAGATTCTGAAGGCCCGGGATTATTATCACAGCATAGGAATTTTGCAC
AGAGACGTGAAGTCCCATAATGTCATCATGATTGATCATGAGCACAGGAAGCTATGACTAAGAGATTGGGATATGGCTGA
GTTTTACCATCATGGCCAAGAATATAATGTCAGAGTTGCTTCACCATACGTCAGAGGTCCTGAGCTACTTGTAGACTATC
AGATGTATGATTATAGTTTGGATATGTGGAAATTGGGTTGTATGCTGGCAAGTATGATCTTCTGGAAAGAGCCATTTTTC
CACGGACATGACAATTATGATCAATTGGTGTGGATAGCCAAGGTTCAGGAACAGAAGATTTATAGGACTCTATTGACAAA
TACAACATTGAATTAGATCCACATTTCAACTATATCTTGGGCAGACACTCCCAGAAGCAATGGGAACACTTTGTCCGCAG
TGAAAACCTGCACCTTGTCAGCCCTGAAGCCTTGGATTTCATGGATAAGTTGCTGCAATATGATCACCAGTCACGACTCG
CTGCAACAGAGGCCATGAAGTACTCCTATTTCTATACTGTTGTGAAGGACTAGTCTCAAATGGGCTCATCTAATATG

Alignment

ORF - retro_cfam_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 67.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKAL
          .K..K.EIKILENL.G.PNIIT.ADIVKDPVS.T.ALVFEH.NNTDF.QLY..LTDYDI.FYMYEILKA.
Retrocopy RKPVKGEIKILENL*GSPNIITMADIVKDPVS*TLALVFEHINNTDFEQLYRMLTDYDILFYMYEILKAR

Parental  DYCHSMGIMHRDVKPHNV-MIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSL
          DY.HS.GI.HRDVK.HNV.MIDHEHRKL.L.DW..AEFYH.GQEYNVRVAS.Y..GPELLVDYQMYDYSL
Retrocopy DYYHSIGILHRDVKSHNVIMIDHEHRKL*LRDWDMAEFYHHGQEYNVRVASPYVRGPELLVDYQMYDYSL

Parental  DMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKV-LGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWE
          DMW.LGCMLASMIF.KEPFFHGHDNYDQLV.IAKV..GTEDL.D.IDKYNIELDP.FN.ILGRHS.K.WE
Retrocopy DMWKLGCMLASMIFWKEPFFHGHDNYDQLVWIAKV<SGTEDL*DSIDKYNIELDPHFNYILGRHSQKQWE

Parental  RFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSM
          .FV.SEN.HLVSPEALDF.DKLL.YDHQSRL.A.EAM...YFYTVVKD...MGSS.M
Retrocopy HFVRSENLHLVSPEALDFMDKLLQYDHQSRLAATEAMKYSYFYTVVKD*SQMGSSNM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	54.98 RPM
SRP017611_brain	0.00 RPM	46.52 RPM
SRP017611_kidney	0.00 RPM	26.02 RPM
SRP017611_liver	0.00 RPM	30.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1408 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006946	1 retrocopy	retro_cfam_1408 ,
Homo sapiens	ENSG00000101266	1 retrocopy	retro_hsap_53,
Mus musculus	ENSMUSG00000074698	3 retrocopies	retro_mmus_1177, retro_mmus_2364, retro_mmus_377,
Otolemur garnettii	ENSOGAG00000002709	1 retrocopy	retro_ogar_820,