RetrogeneDB ID:

retro_btau_49

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:91544108..91545119(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000039794
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CSNK1A1
Ensembl ID:ENSBTAG00000005326
Aliases:None
Description:Casein kinase I isoform alpha [Source:UniProtKB/Swiss-Prot;Acc:P67827]


Retrocopy-Parental alignment summary:






>retro_btau_49
ATGGCGAGCAGCAGCAGACCCAAAACTGATGTCCTTGTCGGAGGAAGATATAAACTGGTACGGGAAATTGGTTTTGGCTC
CTTTGGGCACGTGTATTTGGCGATAGACCTCACCAACCACGAGCAGGTGGCAGTAAAATTAGAATCGGAGAATACCAGGC
AGCCGCGATTGCTACATGAGAAGGAACTCTATAATTTTCTTCAAGGTGGGGTTGGCATCCCCCAGATACGGTGGTATGGT
CAGGAAACTGACTATAATGTGCTAGTGATGGATCTTTTGGGACCCAGCCTTGAAGATCTCTTCAATTTCTGTTCAAGAAG
GTTCTCAATGAAAACTGTACTTATGTTAGCTGATCAGATGATAAGTAGAATCGAATATGTGCATTCCCGCAATCTTATAC
ACAGGGACATTAAACCAGATAACTTCCTAATGGGTACTGGCCCACAGTGGAAGAAATTATTCCTTGTTGATTTTGGTTTG
GCCAAGAAGTACAGAGACAACAGAACAGGGCAACACATACCCCACAGATCTGGTAAAAGTTTCATTGGCACTCCTTTTTG
TGCTAGCATCAGTGCCCATCTTGGTATTGAACAGAGTCGCCGAGATGACATGGAATCAATAGGATATGTTTTGATGTATT
TTAATAGAGGCAGCCTGCCATGGCAAGGCCTAAAAGCTGCAACATTGAAGCAAAAATGTGAAAAGATCAGTGAAATGAAG
ATGACCACACCAGTTGATGTTTTATGTAAGGGATTTCCTATAGAATTTGCCATGTACCTAAAGTATTGTCTCAGGCTGTC
CTTTGAGGAAGCCCCAGATTACAGGTACCTAAGACAGCTTTTTCGGTTGCTTTTCCGAAAACTGAGTTACCAACATGATT
ATGCATTTGATTGGATAGTGTTAAAACAGAAAGCAGAACAGCAGGCTTCCTCTTCAAGTGGGGAGGGTCAGCAGGCCCAA
ACCCCCACAGGCAAAAGTGACAACACCAAAAGTGAAATGAAACATTCTTAA

ORF - retro_btau_49 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.37 %
Parental protein coverage: 97.9 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
MASSS..K....VGG.YKLVR.IG.GSFG..YLAI..TN.E.VAVKLES...R.P.LL.E..LY..LQGG
RetrocopyMASSSRPKTDVLVGGRYKLVREIGFGSFGHVYLAIDLTNHEQVAVKLESENTRQPRLLHEKELYNFLQGG
ParentalVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
VGIP.IRWYGQE.DYNVLVMDLLGPSLEDLFNFCSRRF.MKTVLMLADQMISRIEYVH..N.IHRDIKPD
RetrocopyVGIPQIRWYGQETDYNVLVMDLLGPSLEDLFNFCSRRFSMKTVLMLADQMISRIEYVHSRNLIHRDIKPD
ParentalNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
NFLMG.G....KLFL.DFGLAKKYRDNRT.QHIP.R..K...GT...ASI.AHLGIEQSRRDDMES.GYV
RetrocopyNFLMGTGPQWKKLFLVDFGLAKKYRDNRTGQHIPHRSGKSFIGTPFCASISAHLGIEQSRRDDMESIGYV
ParentalLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
LMYFNR.SLPWQGLKAAT.KQK.EKISE.KM.TPV.VLCKGFP.EFAMYL.YC..L.FEEAPDY.YLRQL
RetrocopyLMYFNRGSLPWQGLKAATLKQKCEKISEMKMTTPVDVLCKGFPIEFAMYLKYCLRLSFEEAPDYRYLRQL
ParentalFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGLKD
FR.LFR.L..Q.DY.FDW..LKQKA.QQA.SSSG.GQQAQTPTG..D
RetrocopyFRLLFRKLSYQHDYAFDWIVLKQKAEQQASSSSGEGQQAQTPTGKSD

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 7 .93 RPM 15 .57 RPM
ERP005899_muscle 0 .84 RPM 88 .26 RPM
SRP017611_brain 4 .70 RPM 44 .40 RPM
SRP017611_kidney 3 .67 RPM 68 .04 RPM
SRP017611_liver 1 .13 RPM 38 .66 RPM
SRP030211_testis 6 .99 RPM 143 .88 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_49 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_49 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_49 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000005326 2 retrocopies
retro_btau_1662, retro_btau_49 ,
Bos taurus ENSBTAG000000175501 retrocopy
retro_btau_1659,
Canis familiaris ENSCAFG000000182861 retrocopy
retro_cfam_1887,
Callithrix jacchus ENSCJAG000000211211 retrocopy
retro_cjac_2680,
Homo sapiens ENSG000001137121 retrocopy
retro_hsap_32,
Gorilla gorilla ENSGGOG000000139263 retrocopies
retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus ENSMLUG000000029104 retrocopies
retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta ENSMMUG000000017582 retrocopies
retro_mmul_2207, retro_mmul_295,
Monodelphis domestica ENSMODG000000099371 retrocopy
retro_mdom_2005,
Oryctolagus cuniculus ENSOCUG000000066697 retrocopies
retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Otolemur garnettii ENSOGAG000000032532 retrocopies
retro_ogar_1195, retro_ogar_825,
Sorex araneus ENSSARG000000114461 retrocopy
retro_sara_518,
Sarcophilus harrisii ENSSHAG000000153561 retrocopy
retro_shar_834,
Sus scrofa ENSSSCG000000144351 retrocopy
retro_sscr_560,
Ictidomys tridecemlineatus ENSSTOG000000221411 retrocopy
retro_itri_1378,
Drosophila melanogaster FBgn00150244 retrocopies
retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,


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