RetrogeneDB ID:

retro_hsap_1882

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:43608196..43609193(+)
Located in intron of:ENSG00000152229
Retrocopy
information
Ensembl ID:ENSG00000267293
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UTP18
Ensembl ID:ENSG00000011260
Aliases:UTP18, CGI-48, WDR50
Description:UTP18 small subunit (SSU) processome component homolog (yeast) [Source:HGNC Symbol;Acc:24274]


Retrocopy-Parental alignment summary:






>retro_hsap_1882
ATGCCGCGGGAACTGAGGAGCCGAATGAAACTGCACAGTAGAACCGCAGCGAAGCCGAAGCGTTAGCCCGGAACGAGGGC
GGACTGGAAAGCCGGAGCGGGGCCGAGCGAGCCGCCCCAAAAGGCTGCCGCTTCATCCCAGCGAAAACCGCCGGCCAGGC
CAAGCGCGGCGAGGGAAGAGGAGAGACGGCTCCGGCAGCGGAACCGCCCGACGCTGGAGAAGACAAACCGGCCGTGGAGT
GGTGCCTGGAGGAGCTGGTCTTCGGCGATGTCGAGGACGACGAGGACACGCTGCTGCGGCGTCTGCGGGGTCCGTGGGTT
CAAGGACATGAAGACTTGGGAGACTCAGAAGCGGAGAATGAAGCAAAAGGTAATTGTGCACCTCAAAAGAAGCCAATTTG
GGTGGATGAAGAAGATGAAGATGAGGAAATGGTTGACATGATGAACAATCGGTTTCGGAAAGATAATGATGAAAAATGCT
AGTGAAAGTAAACTTTAGAAAGACAAACTTAAGAAGCGACTTTAAGAAGAATTCCAGCATGCCGTGGGAGGAGTACCTGC
CTGGGCAGAGACTAATAAGCTGAAAACAACTTCAGATGATGAAAGTGAAGAGGATGAAGATGCTTTGTTGCAAAGGACTG
GGAATTTCATATCCACATCAACTTCTCTTCCAAGAGGAATCCTGAAGATGAAGAACTGCCAGCATGGTAATGCTGAACGT
CCTTCTGCTGCTCAGATCTCATCTGTGCAGTTCCGTCCTTGTGCACAGATTGTGATGGTCGCTGGATTAGATAACCTATA
TCACTATTTCAGGTTGATGGAAGAACAAATCCTAAAATCCAGAGCACCTGTTTGGAAAGGTTTCCAAACTGTAAGGCTTA
TTTTAGTGCTAATGGGGAAGAAGTTTTAGCCATGAGTACTCACAGCAAGGTTTTTTATGTCTATGACATGCTAGCTGGAA
ATTAATTCCTGTGCATCAAGTGAGAGGTTTGAAAGAA

ORF - retro_hsap_1882 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.26 %
Parental protein coverage: 61.33 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMPPERRRRMKLDRRTGAKPKRKPGMRPDWKAGAGPGGPPQKPAPSSQRKPPARPSAAAAAIAVAAAEEER
MP.E.R.RMKL..RT.AKPKR.PG.R.DWKAGAG....P..P...........P.A.......AA.EEER
RetrocopyMPRELRSRMKLHSRTAAKPKR*PGTRADWKAGAG----PSEPPQKAAASSQRKPPARPS----AAREEER
ParentalRLRQRNRLRLE-EDKPAVERCLEELVFGDVENDEDALLRRLRGPRVQEHEDSGDSEVENEAKGNFPPQKK
RLRQRNR..LE.EDKPAVE.CLEELVFGDVE.DED.LLRRLRGP.VQ.HED.GDSE.ENEAKGN..PQKK
RetrocopyRLRQRNRPTLE<EDKPAVEWCLEELVFGDVEDDEDTLLRRLRGPWVQGHEDLGDSEAENEAKGNCAPQKK
ParentalPVWVDEEDEDEEMVDMMNNRFRKD-MMKNASESKLSKDNLKKRLKEEFQHAMGGVPAWAETTKRKTSSDD
P.WVDEEDEDEEMVDMMNNRFRKD.MMKNASESKL.KD.LKKRL.EEFQHA.GGVPAWAET.K.KT.SDD
RetrocopyPIWVDEEDEDEEMVDMMNNRFRKD>MMKNASESKL*KDKLKKRL*EEFQHAVGGVPAWAETNKLKTTSDD
ParentalESEEDEDDLLQRTGNFISTSTSLPRGILKMKNCQHANAERPTVARISSVQFHPGAQIVMVAGLDN-AVSL
ESEEDED.LLQRTGNFISTSTSLPRGILKMKNCQH.NAERP..A.ISSVQF.P.AQIVMVAGLDN...SL
RetrocopyESEEDEDALLQRTGNFISTSTSLPRGILKMKNCQHGNAERPSAAQISSVQFRPCAQIVMVAGLDN<PISL
ParentalFQVDGKTNPKIQSIYLERFPIFKACFSANGEEVLATSTHSKVLYVYDMLAG-KLIPVHQVRGLKE
FQVDG.TNPKIQS..LERFP..KA.FSANGEEVLA.STHSKV.YVYDMLAG.KLIPVHQVRGLKE
RetrocopyFQVDGRTNPKIQSTCLERFPNCKAYFSANGEEVLAMSTHSKVFYVYDMLAG<KLIPVHQVRGLKE

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 20 .41 RPM
bodymap2_adrenal 0 .06 RPM 34 .14 RPM
bodymap2_brain 0 .00 RPM 31 .25 RPM
bodymap2_breast 0 .06 RPM 18 .46 RPM
bodymap2_colon 0 .10 RPM 23 .45 RPM
bodymap2_heart 0 .00 RPM 6 .92 RPM
bodymap2_kidney 0 .00 RPM 37 .58 RPM
bodymap2_liver 0 .00 RPM 16 .41 RPM
bodymap2_lung 0 .00 RPM 31 .68 RPM
bodymap2_lymph_node 0 .00 RPM 28 .36 RPM
bodymap2_ovary 0 .02 RPM 43 .01 RPM
bodymap2_prostate 0 .14 RPM 29 .77 RPM
bodymap2_skeletal_muscle 0 .00 RPM 25 .04 RPM
bodymap2_testis 0 .60 RPM 82 .78 RPM
bodymap2_thyroid 0 .00 RPM 45 .46 RPM
bodymap2_white_blood_cells 0 .02 RPM 44 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1882 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_1882 retrocopy
EST ID Start End Identity Match Mis-match Score
DB020852 43608192 43608745 99.9 552 1 551
DB025259 43608186 43608470 98.3 281 2 278

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_673271502 libraries298 libraries29 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_1882 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_1882 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1882 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1379
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000014771 retrocopy
retro_cpor_657,
Homo sapiens ENSG00000011260 1 retrocopy
retro_hsap_1882 ,
Gorilla gorilla ENSGGOG000000170611 retrocopy
retro_ggor_1379,
Myotis lucifugus ENSMLUG000000169381 retrocopy
retro_mluc_2308,
Mustela putorius furoENSMPUG000000155821 retrocopy
retro_mputfur_646,
Vicugna pacos ENSVPAG000000101641 retrocopy
retro_vpac_170,

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 = 0.21 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .19 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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