RetrogeneDB ID:

retro_hsap_32

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:37678379..37679393(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000180138
Aliases:CSNK1A1L, CK1
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CSNK1A1
Ensembl ID:ENSG00000113712
Aliases:CSNK1A1, CK1, CK1a, CKIa, HEL-S-77p, HLCDGP1, PRO2975
Description:casein kinase 1, alpha 1 [Source:HGNC Symbol;Acc:2451]


Retrocopy-Parental alignment summary:






>retro_hsap_32
ATGACAAACAACAGCGGCTCCAAAGCCGAACTCGTTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC
CTTTGGAGACGTTTATCTGGGCATCACCACCACCAACGGCGAGGACGTAGCAGTGAAGCTGGAATCTCAGAAGGTCAAGC
ACCCCCAGTTGCTGTATGAGAGCAAACTCTACACGATTCTTCAAGGTGGGGTTGGCATCCCCCACATGCACTGGTATGGT
CAGGAAAAAGACAACAATGTGCTAGTCATGGACCTTCTGGGACCCAGCCTCGAAGACCTCTTTAATTTCTGTTCAAGAAG
GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGCAGAATTGAATACGTGCATACAAAGAATTTTCTAC
ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGTCACTGTAATAAGTTGTTCCTTATTGATTTTGGTTTG
GCCAAAAAGTACAGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA
TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT
TTAATAGAACCAGCCTGCCGTGGCAAGGACTAAGGGCTATGACAAAAAAACAAAAATATGAAAAGATTAGTGAGAAGAAG
ATGTCCACCCCTGTTGAAGTTTTATGTAAGGGGTTTCCTGCAGAATTCGCCATGTACTTGAACTACTGTCGTGGGCTGCG
CTTTGAGGAAGTCCCAGATTACATGTATCTGAGGCAGCTATTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT
ACACATTTGATTGGACGATGTTAAAGCAGAAAGCAGCACAGCAGGCAGCCTCTTCCAGTGGGCAGGGTCAGCAGGCCCAA
ACCCAGACAGGCAAGCAAACTGAAAAAAACAAGAATAATGTGAAAGATAACTAA

ORF - retro_hsap_32 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.04 %
Parental protein coverage: 99.41 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
M...SGSKAE..VGGKYKLVRKIGSGSFGD.YL.I..TNGE.VAVKLESQK..HPQLLYESKLY.ILQGG
RetrocopyMTNNSGSKAELVVGGKYKLVRKIGSGSFGDVYLGITTTNGEDVAVKLESQKVKHPQLLYESKLYTILQGG
ParentalVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
VGIPH..WYGQEKD.NVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNF.HRDIKPD
RetrocopyVGIPHMHWYGQEKDNNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFLHRDIKPD
ParentalNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
NFLMG.GRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDK.L.GT.RYASINAHLGIEQSRRDDMESLGYV
RetrocopyNFLMGTGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYV
ParentalLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
.MYFNRTSLPWQGL.A.TKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEE.PDYMYLRQL
RetrocopyFMYFNRTSLPWQGLRAMTKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQL
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
bodymap2_adipose 0 .02 RPM 101 .52 RPM
bodymap2_adrenal 0 .00 RPM 68 .80 RPM
bodymap2_brain 0 .07 RPM 65 .09 RPM
bodymap2_breast 0 .00 RPM 69 .55 RPM
bodymap2_colon 0 .00 RPM 75 .87 RPM
bodymap2_heart 0 .00 RPM 66 .11 RPM
bodymap2_kidney 0 .00 RPM 58 .63 RPM
bodymap2_liver 0 .00 RPM 30 .67 RPM
bodymap2_lung 0 .09 RPM 103 .55 RPM
bodymap2_lymph_node 0 .00 RPM 51 .86 RPM
bodymap2_ovary 0 .00 RPM 90 .33 RPM
bodymap2_prostate 0 .00 RPM 74 .72 RPM
bodymap2_skeletal_muscle 0 .00 RPM 79 .77 RPM
bodymap2_testis 4 .03 RPM 71 .62 RPM
bodymap2_thyroid 0 .00 RPM 98 .17 RPM
bodymap2_white_blood_cells 0 .00 RPM 95 .90 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_32 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_32 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_32 retrocopy 5' end.

Lab - click to see more details

retro_hsap_32 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_32 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_7
Gorilla gorilla retro_ggor_984
Pongo abelii retro_pabe_170
Macaca mulatta retro_mmul_295
Callithrix jacchus retro_cjac_2680
Parental genes homology:
Parental genes homology involve 14 parental genes, and 30 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 ENSG00000113712 1 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,
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,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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