RetrogeneDB ID:

retro_mmul_295

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:17:16307573..16308587(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000005012
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CSNK1A1
Ensembl ID:ENSMMUG00000001758
Aliases:None
Description:casein kinase I isoform alpha [Source:RefSeq peptide;Acc:NP_001248164]


Retrocopy-Parental alignment summary:






>retro_mmul_295
ATGGCAAACAACAGCGGCTCCAAGGCCGAACTCGTTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC
CTTCGGAGACGTTTATCTGGGGATCACCACCACCAACGGCGAGGAAGTAGCAGTGAAGCTGGAATCTCAGAAGGCCAAGC
ACCCCCAGTTGTTATATGAGAGCAAACTCTACACGATTCTTCAAGGTGGGGTTGGCATCCCCCACATGCACTGGTATGGT
CAGGAAAAAGACAGCAATGTGCTAGTCATGGACCTTCTGGGACCCAGCCTCGAAGACCTCTTTAATTTCTGTTCAAGAAG
GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGCAGAATTGAATACGTGCATACAAAGAATTTTCTAC
ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGCCACTGTAACAAGTTGTTCCTTATTGATTTTGGTTTG
GCCAAAAAGTACAGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA
TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT
TTAATAGAACCAGCCTGCCGTGGCAAGGACTAAAGGCTATAACAAAAAAACAAAAATATGAAAAAATTAGTGAGAAGAAG
ATGTCCACCCCTGTTGAAGTTTTATGTAAGGGGTTTCCTGCAGAATTCGCCATGTACTTGAACTACTGTCGTGGGCTGCG
CTTTGAGGAAGTCCCAGATTACATGTATCTGAGGCAGCTATTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT
ACACATTTGATTGGACGATGTTAAAGCAGAAAGCAGCACAGCAGGCAGCCTCTTCCAGTGGGCAGGGTCAGCAGGCCCAA
ACCCAGACAGGCAAGCAAACTGAAAAAAACAAGAATAATGTGAAAGAAAACTAA

ORF - retro_mmul_295 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.24 %
Parental protein coverage: 99.41 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
MA..SGSKAE..VGGKYKLVRKIGSGSFGD.YL.I..TNGEEVAVKLESQKA.HPQLLYESKLY.ILQGG
RetrocopyMANNSGSKAELVVGGKYKLVRKIGSGSFGDVYLGITTTNGEEVAVKLESQKAKHPQLLYESKLYTILQGG
ParentalVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
VGIPH..WYGQEKD.NVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNF.HRDIKPD
RetrocopyVGIPHMHWYGQEKDSNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFLHRDIKPD
ParentalNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
NFLMG.GRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDK.L.GT.RYASINAHLGIEQSRRDDMESLGYV
RetrocopyNFLMGTGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYV
ParentalLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
.MYFNRTSLPWQGLKA.TKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEE.PDYMYLRQL
RetrocopyFMYFNRTSLPWQGLKAITKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQL
ParentalFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDKTKSNMK
FRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQT.TGKQT.K.K.N.K
RetrocopyFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTQTGKQTEKNKNNVK

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
SRP007412_brain 0 .00 RPM 71 .26 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 67 .43 RPM
SRP007412_cerebellum 0 .00 RPM 90 .15 RPM
SRP007412_heart 0 .06 RPM 59 .12 RPM
SRP007412_kidney 0 .00 RPM 68 .19 RPM
SRP007412_liver 0 .00 RPM 29 .89 RPM
SRP007412_testis 37 .32 RPM 69 .47 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_295 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_295 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_295 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_32
Pan troglodytes retro_ptro_7
Gorilla gorilla retro_ggor_984
Pongo abelii retro_pabe_170
Callithrix jacchus retro_cjac_2680
Parental genes homology:
Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000053262 retrocopies
retro_btau_1662, retro_btau_49,
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 ENSMMUG00000001758 2 retrocopies
retro_mmul_2207, retro_mmul_295 ,
Macaca mulatta ENSMMUG000000066201 retrocopy
retro_mmul_1195,
Macaca mulatta ENSMMUG000000066461 retrocopy
retro_mmul_1040,
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,
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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