RetrogeneDB ID:

retro_hsap_53

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:11373490..11374666(-)
Located in intron of:ENSG00000110328
Retrocopy
information
Ensembl ID:ENSG00000254598
Aliases:CSNK2A3, CSNK2A1P
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CSNK2A1
Ensembl ID:ENSG00000101266
Aliases:None
Description:casein kinase 2, alpha 1 polypeptide [Source:HGNC Symbol;Acc:2457]


Retrocopy-Parental alignment summary:






>retro_hsap_53
ATGTCGGGACCCGTGCCAAGCAGGGCCAGAGTTTACACAGATGTTAATACACACAGACCTCGAGAATACTGGGATTACGA
GTCACATGTGGTGGAATGGGGAAATCAAGATGACTACCAGCTGGTTCGAAAATTAGGCCGAGGTAAATACAGTGAAGTAT
TTGAAGCCATCAACATCACAAATAATGAAAAAGTTGTTGTTAAAATTCTCAAGCCAGTAAAAAAGAAGAAAATTAAGCGT
GAAATAAAGATTTTGGAGAATTTGAGAGGAGGTCCCAACATCATCACACTGGCAGACATTGTAAAAGACCCTGTGTCACG
AACCCCCGCCTTGGTTTTTGAACACGTAAACAACACAGACTTCAAGCAATTGTACCAGACGTTAACAGACTATGATATTC
GATTTTACATGTATGAGATTCTGAAGGCCCTGGATTATTGTCACAGCATGGGAATTATGCACAGAGATGTCAAGCCCCAT
AATGTCATGATTGATCATGAGCACAGAAAGCTACGACTAATAGACTGGGGTTTGGCTGAGTTTTATCATCCTGGCCAAGA
ATATAATGTCCGAGTTGCTTCCCGATACTTCAAAGGTCCTGAGCTACTTGTAGACTATCAGATGTACGATTATAGTTTGG
ATATGTGGAGATTGGGTTGTATGCTGGCAAGTATGATCTTTCGGAAGGAGCCATTTTTCCATGGACGTGACAATTATGAT
CAGTTGGTGAGGATAGCCAAGTTTCTGGGGACAGAAGATTTATATGGCTATATTGACAAATACAACATTGAATTAGATCC
ACGTTTCAATGATATCTTGGGCAGACACTCTCGAAAGCGATGGGAACGCTTTGTCCACAGTGAAAATCAGCACCTTGTCA
GCCCTGAGGCCTTGGATTTCCTGGACAAACTGCTGCGATATGACCACCAGTCACGGCTTACTGCAAGAGAGGCCATGGAG
CACCCCTATTTCTACACTGTTGTGAAGGACCAGGCTCGAATGGGTTCATCTAGCATGCCAGGGGGCAGTACGCCCGTCAG
CAGCGCCAATGTGATGTCAGGGATTTCTTCAGTGCCAACTCCTTCACCCCTTGGACCTCTGGCAGGCTCACCAGTGATTG
CTGCTGCCAACCCCCTTGGGATGCCTGTTCCAGCTGCCACTGGCGCTCAGCAGTAA

ORF - retro_hsap_53 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.47 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
RetrocopyMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
ParentalKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
RetrocopyKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
ParentalLKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
RetrocopyLKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
ParentalYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR
YSLDMW.LGCMLASMIFRKEPFFHG.DNYDQLVRIAK.LGTEDLY.YIDKYNIELDPRFNDILGRHSRKR
RetrocopyYSLDMWRLGCMLASMIFRKEPFFHGRDNYDQLVRIAKFLGTEDLYGYIDKYNIELDPRFNDILGRHSRKR
ParentalWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSAN
WERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSAN
RetrocopyWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSAN
ParentalMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ
.MSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAA.GAQQ
RetrocopyVMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAATGAQQ

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 .34 RPM 86 .67 RPM
bodymap2_adrenal 0 .14 RPM 74 .55 RPM
bodymap2_brain 0 .16 RPM 75 .10 RPM
bodymap2_breast 0 .12 RPM 76 .23 RPM
bodymap2_colon 0 .02 RPM 78 .91 RPM
bodymap2_heart 0 .31 RPM 76 .43 RPM
bodymap2_kidney 0 .12 RPM 92 .15 RPM
bodymap2_liver 0 .08 RPM 36 .99 RPM
bodymap2_lung 0 .04 RPM 62 .11 RPM
bodymap2_lymph_node 0 .04 RPM 74 .98 RPM
bodymap2_ovary 0 .42 RPM 122 .68 RPM
bodymap2_prostate 0 .14 RPM 94 .08 RPM
bodymap2_skeletal_muscle 0 .56 RPM 175 .69 RPM
bodymap2_testis 0 .38 RPM 130 .03 RPM
bodymap2_thyroid 0 .47 RPM 108 .07 RPM
bodymap2_white_blood_cells 0 .06 RPM 106 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_53 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_53 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_9910703 libraries795 libraries318 libraries11 libraries2 libraries

The graphical summary, for retro_hsap_53 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_53 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_53 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 7 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000140392 retrocopies
retro_amel_138, retro_amel_1888,
Canis familiaris ENSCAFG000000069461 retrocopy
retro_cfam_1408,
Homo sapiens ENSG00000101266 1 retrocopy
retro_hsap_53 ,
Mus musculus ENSMUSG000000746983 retrocopies
retro_mmus_1177, retro_mmus_2364, retro_mmus_377,
Otolemur garnettii ENSOGAG000000027091 retrocopy
retro_ogar_820,
Sorex araneus ENSSARG0000000289610 retrocopies
retro_sara_188, retro_sara_189, retro_sara_240, retro_sara_357, retro_sara_468, retro_sara_508, retro_sara_534, retro_sara_572, retro_sara_738, retro_sara_755,
Tursiops truncatus ENSTTRG000000070641 retrocopy
retro_ttru_1605,

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 = 1.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .17 RPM
CEU_NA11930 0 .49 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .29 RPM
CEU_NA12760 0 .67 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .33 RPM
CEU_NA12873 0 .26 RPM
FIN_HG00183 0 .33 RPM
FIN_HG00277 0 .30 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .45 RPM
FIN_HG00328 0 .36 RPM
FIN_HG00338 0 .23 RPM
FIN_HG00349 0 .57 RPM
FIN_HG00375 0 .27 RPM
FIN_HG00377 0 .18 RPM
FIN_HG00378 0 .25 RPM
GBR_HG00099 0 .46 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .21 RPM
GBR_HG00119 0 .29 RPM
GBR_HG00131 0 .46 RPM
GBR_HG00133 0 .22 RPM
GBR_HG00134 0 .33 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .31 RPM
GBR_HG00143 0 .32 RPM
TSI_NA20512 0 .20 RPM
TSI_NA20513 0 .44 RPM
TSI_NA20518 0 .94 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .46 RPM
TSI_NA20756 0 .67 RPM
TSI_NA20765 0 .27 RPM
TSI_NA20771 0 .54 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 1 .05 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .25 RPM
YRI_NA19093 0 .31 RPM
YRI_NA19099 0 .64 RPM
YRI_NA19114 0 .31 RPM
YRI_NA19118 0 .21 RPM
YRI_NA19213 0 .41 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .44 RPM

Indel association:

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



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