RetrogeneDB ID:

retro_btau_1662

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:8:97126432..97127407(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000046079
Aliases:None
Status:KNOWN_PSEUDOGENE
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_1662
ATGGGGAGTAGCAGCGGCTCCAAGGCCGAATTCATTGTCGGAGGCAAATACAAACTGGTACGGAAGATCAGGTCTGGCTC
CTTCGGGGACATGTATTTAGCGATCAACATCACCAACGGTGAGGAGGTGGCAGTGAAGCTAGAATCCCAGAAGGCCAGGC
ATCCCCAGTTGCTGTACGAGAGCAAACTCTGTAAGATTCTTCAAGGTGAGGTTGGCATCCCCCACATAAGGTGGTATGGT
CAGCAAAAAGACTATAACGTGCTAGTTATGGATCTTCTTGGACCCAGCCTTGAAGACCTCTTCAATTTCTGTTCAAGAAG
GTTCACAATGAAAACTGTACTTATGTTAGCTGACCAGATGATGGGTAGAATTGAATATGTGCATACAAAGAATTTTATAC
ACAGAGACATTAAACCAGATAACTTCCTAATGGGTATTGGGCGTCACTGTAATAAGTTGTTCCTTATTGATTTTGGTTTG
GCCAAAAAGTACAGAGACAACAGGACAAGGCAACACATACCATACAGAGAAGATAAAAATCTCACTGGCACTGCTCGGTA
TGCTAGCATCAGTGCACATCTTGGTATTGAACAAAGTCGCCGAGATGACATGGAATCATTAGGATATGTTTTGATGTATT
TTAATAGAACCAGCCTGCCATGGCAAGGACTAAAGGCTGCAACAAAAAAGCAAAAATATGAAAAAATTAGCGAAAAGAAG
ATGTCCACACCTGTTGAAGTTTTATGTAAGGGATTTCCTGCAGAATTTGCCATGTACTTAAACTATTGTCGTGGGCTGCG
CTTTGAGGAAGCCCCGGATTACATGTACCTGAGGCACCTATTCCACATTCTTTTCAGGACCCTGAATCACCAATATGACT
ACACATCTGATTGGACAATGTTAAAGCAGAAAGCAGCACAGCAGGCAGCCTCTTCAAGTGGGCAGGGTCAGCAGGCCCAA
ACCCCCACAGGTTTC

ORF - retro_btau_1662 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.62 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
M.SSSGSKAEFIVGGKYKLVRKI.SGSFGD.YLAINITNGEEVAVKLESQKARHPQLLYESKL.KILQG.
RetrocopyMGSSSGSKAEFIVGGKYKLVRKIRSGSFGDMYLAINITNGEEVAVKLESQKARHPQLLYESKLCKILQGE
ParentalVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
VGIPHIRWYGQ.KDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQM..RIEYVHTKNFIHRDIKPD
RetrocopyVGIPHIRWYGQQKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMMGRIEYVHTKNFIHRDIKPD
ParentalNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
NFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASI.AHLGIEQSRRDDMESLGYV
RetrocopyNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASISAHLGIEQSRRDDMESLGYV
ParentalLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
LMYFNRTSLPWQGLKAA............KMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLR.L
RetrocopyLMYFNRTSLPWQGLKAAXXXXXXXXXXXXKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRHL
ParentalFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGF
F.ILFRTLNHQYDYT.DWTMLKQKAAQQAASSSGQGQQAQTPTGF
RetrocopyFHILFRTLNHQYDYTSDWTMLKQKAAQQAASSSGQGQQAQTPTGF

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 0 .00 RPM 15 .57 RPM
ERP005899_muscle 0 .21 RPM 88 .26 RPM
SRP017611_brain 0 .23 RPM 44 .40 RPM
SRP017611_kidney 0 .47 RPM 68 .04 RPM
SRP017611_liver 0 .15 RPM 38 .66 RPM
SRP030211_testis 0 .27 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_1662 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1662 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1662 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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