RetrogeneDB ID:

retro_hsap_186

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:92591256..92592020(+)
Located in intron of:ENSG00000189195
Retrocopy
information
Ensembl ID:ENSG00000233401
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRKAR1A
Ensembl ID:ENSG00000108946
Aliases:PRKAR1A, ACRDYS1, ADOHR, CAR, CNC, CNC1, PKR1, PPNAD1, PRKAR1, TSE1
Description:protein kinase, cAMP-dependent, regulatory, type I, alpha [Source:HGNC Symbol;Acc:9388]


Retrocopy-Parental alignment summary:






>retro_hsap_186
TCTTTAGCCAAAGCCATTGAAAAGAATGTGCTGATTTCACATCTTGATGATAATGAGAGAAGTGATATATTTGATGCCAT
ATTTCCATGTCTCCTTTATCACTGGAGAGAGACAGTGATTCTGCAAGGTGATGAAGGGGATAACTTCTAGGTGATTGAGC
AAGGAGAGAGGGATGTCTGTGTCAATGATGAATGAGCAACCAGTGTTGAAGAAGGAGGGAGCTTTGGAGAATTTGTTTTG
ATTTATGGAACACCTAGAGTAGCCACTGTCAAAGCAAAGGCAAATGTGAAATGGTAGTGTATCAACCGAGGCAGCTGTAG
AAGAATCCATATGGGAAGCACACTGAGAATGTGGAAGATGTATGAGGAATTCCTTAGTAAAGTGTCTATTTTAGAGTCTC
TGGATAAGTGAAAGCATCTTACGGTAGCTGATACATGGGAACCAGTCAAGTTTGAAGATTGGCAGAAGATTGTGGTGCAG
GGAGAACCAGGGGATGAGTTCCTTATTATTCTAGAGGGGCCAGCTGCTATGCTGCAACGTTGATAAGAAAATGAAGAGTT
TGTTGAAGTGGGAAGATTGGGGCCTTCTGATTATTTTGGTGAATTTGCATTCCTGATGAATCACCCTCCTGCTGCCACAG
TGGTTGTACATGGCCCCTTGAAGTACATTAAGCTGGACCAGCCTAGATTTGAATGTGCTCTTGCCCAGGCTCAGACCTCC
TCAAACGAAACATCCAGCAGTACAACAGTTTTGTGTCACTGTCT

ORF - retro_hsap_186 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.95 %
Parental protein coverage: 66.67 %
Number of stop codons detected: 6
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalALAKAIEKNVLFSHLDDNERSDIFDAMFS-VSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVG
.LAKAIEKNVL.SHLDDNERSDIFDA.F........ETVI.QGDEGDNF.VI.QGE.DV.VN.E.ATSV.
RetrocopySLAKAIEKNVLISHLDDNERSDIFDAIFPCLLYHWRETVILQGDEGDNF*VIEQGERDVCVNDE*ATSVE
ParentalEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERL
EGGSFGE..LIYGTPR.ATVKAK.NVK...I.R.S.RRI.MGSTLR..KMYEEFLSKVSILESLDK...L
RetrocopyEGGSFGEFVLIYGTPRVATVKAKANVKW*CINRGSCRRIHMGSTLRMWKMYEEFLSKVSILESLDK*KHL
ParentalTVADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPR
TVAD..EPV.FED.QKIVVQGEPGDEF.IILEG.AA.LQR..ENEEFVEVGRLGPSDYFGE.A.LMN.P.
RetrocopyTVADTWEPVKFEDWQKIVVQGEPGDEFLIILEGPAAMLQR**ENEEFVEVGRLGPSDYFGEFAFLMNHPP
ParentalAATVVARGPLKCVKLDRPRFERVLG-PCSDILKRNIQQYNSFVSLS
AATVV..GPLK..KLD.PRFE..L..P.SD.LKRNIQQYNSFVSLS
RetrocopyAATVVVHGPLKYIKLDQPRFECALA<PGSDLLKRNIQQYNSFVSLS

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 .00 RPM 839 .98 RPM
bodymap2_adrenal 0 .00 RPM 300 .33 RPM
bodymap2_brain 0 .02 RPM 752 .33 RPM
bodymap2_breast 0 .02 RPM 517 .48 RPM
bodymap2_colon 0 .00 RPM 491 .58 RPM
bodymap2_heart 0 .02 RPM 655 .44 RPM
bodymap2_kidney 0 .00 RPM 473 .87 RPM
bodymap2_liver 0 .00 RPM 177 .71 RPM
bodymap2_lung 0 .00 RPM 658 .51 RPM
bodymap2_lymph_node 0 .00 RPM 380 .38 RPM
bodymap2_ovary 0 .00 RPM 741 .64 RPM
bodymap2_prostate 0 .00 RPM 406 .95 RPM
bodymap2_skeletal_muscle 0 .00 RPM 802 .85 RPM
bodymap2_testis 0 .02 RPM 624 .66 RPM
bodymap2_thyroid 0 .04 RPM 465 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 651 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_186 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_186 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_186 retrocopy 5' end.

Lab - click to see more details

retro_hsap_186 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_186 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_393
Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000108946 1 retrocopy
retro_hsap_186 ,
Gorilla gorilla ENSGGOG000000165071 retrocopy
retro_ggor_267,
Macaca mulatta ENSMMUG000000021942 retrocopies
retro_mmul_2498, retro_mmul_393,
Nomascus leucogenys ENSNLEG000000019821 retrocopy
retro_nleu_996,
Pan troglodytes ENSPTRG000000095791 retrocopy
retro_ptro_172,
Ictidomys tridecemlineatus ENSSTOG000000129031 retrocopy
retro_itri_104,

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 .03 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 .00 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 .00 RPM
FIN_HG00378 0 .00 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 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 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 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 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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