RetrogeneDB ID:

retro_hsap_2724

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:160170257..160171190(+)
Located in intron of:ENSG00000213186
Retrocopy
information
Ensembl ID:ENSG00000244009
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:B3GAT3
Ensembl ID:ENSG00000149541
Aliases:B3GAT3, GLCATI, glcUAT-I
Description:beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I) [Source:HGNC Symbol;Acc:923]


Retrocopy-Parental alignment summary:






>retro_hsap_2724
CTACGCGCTGGCCAGCCATGTGACTGCCTTCCTCCCCTGCGGGCAGCAGCTGAGCAGCTACGGCAGAAGGATCTGAGGAT
TTCCCAGCTGCAAGCGGAACTCCGACGGCCACCCCCTGCCCCTGCCCAGCCCCCTGAACCCGAGGCCCTGCCTACTATCT
ATGTTGTTACCCCCACCTATGCCAGGCTGGTACAGAAGGCAGAGTTGGTACGGCTGTCCCAGACACTGAGCCTGGTGCCC
CGGCTGCATTGACTGCTGGTGGAGGATGCTGAGGGTCCCACCCCGCTGGTCTCAGGGCTGCTGGCTGCCTCTGGCCTCCT
CTTCACACACCTGGTGGTCCTCACGCCCAAAGCCCAGCGGCTTCGGGAGGGCAAGCCTGGCTGGGTTCATCCCCATGGTG
TCGAGCAGCGGAACAAGGCCCTGGACTGGCTCCGGGGCAGAGGGAGTGCTGTGGGTGGGAAGAAGGACCCATCACCACCA
GGGACCCAAGGAGTCGTGTACTTTGCTGACAGTGGCAACACCTACAGCTGGGAGCTGTTTGAGGAGATGCGCTGGACCCG
TGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGAGTCAAGGGCCCTCAGGTACAGGACAGCCGGGTAGTGG
GCTTCCACACAGCATGGGAGCCCAACGGGCCCTTCCCTGTGGATATGGCCGGATTTGCTGTGGCCCTGCCCTTGCTGTTA
GCTAAGCCCAATGCCCAGTTTGATTCCACTGCTCCCCGGAGCCACCTGGAGAGCAGTCTTCTAAGCCACCTTGTGGATCC
CAAGGACCTGGAGCCACGGGCTGCCAACTGCACTCGGGTACTGGTGTGACATACACGGACAGCGAAGCCCAAGATGAAGC
AGAAGGAGCAGCTGCAGCGGCAGGGCCAGGGCTCAGACCCAGCAATTGAGGTG

ORF - retro_hsap_2724 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.6 %
Parental protein coverage: 92.84 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVQLGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
...GQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
RetrocopyLRAGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
ParentalRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKA
RLSQTLSLVPRLH.LLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREG.PGWVHP.GVEQRNKA
RetrocopyRLSQTLSLVPRLH*LLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGKPGWVHPHGVEQRNKA
ParentalLDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDG
LDWLRGRG.AVGG.KDP.PPGTQGVVYFAD..NTYS.ELFEEMRWTRGVSVWPVGLVGGLR..GPQVQD.
RetrocopyLDWLRGRGSAVGGKKDPSPPGTQGVVYFADSGNTYSWELFEEMRWTRGVSVWPVGLVGGLRVKGPQVQDS
ParentalRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRV
RVVGFHTAWEP..PFPVDMAGFAVALPLLL.KPNAQFDSTAPR.HLESSLLSHLVDPKDLEPRAANCTRV
RetrocopyRVVGFHTAWEPNGPFPVDMAGFAVALPLLLAKPNAQFDSTAPRSHLESSLLSHLVDPKDLEPRAANCTRV
ParentalLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV
LV.HTRT.KPKMKQ.EQLQRQG.GSDPAIEV
RetrocopyLV*HTRTAKPKMKQKEQLQRQGQGSDPAIEV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 9 .12 RPM
bodymap2_adrenal 0 .00 RPM 22 .76 RPM
bodymap2_brain 0 .00 RPM 11 .27 RPM
bodymap2_breast 0 .00 RPM 8 .70 RPM
bodymap2_colon 0 .02 RPM 13 .88 RPM
bodymap2_heart 0 .00 RPM 2 .53 RPM
bodymap2_kidney 0 .00 RPM 14 .04 RPM
bodymap2_liver 0 .02 RPM 9 .89 RPM
bodymap2_lung 0 .00 RPM 14 .05 RPM
bodymap2_lymph_node 0 .05 RPM 20 .67 RPM
bodymap2_ovary 0 .00 RPM 18 .95 RPM
bodymap2_prostate 0 .05 RPM 12 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .38 RPM
bodymap2_testis 0 .21 RPM 15 .18 RPM
bodymap2_thyroid 0 .00 RPM 11 .41 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .86 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_2724 was not detected
No EST(s) were mapped for retro_hsap_2724 retrocopy.
No TSS is located nearby retro_hsap_2724 retrocopy 5' end.
retro_hsap_2724 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2724 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1841
Gorilla gorilla retro_ggor_1896
Pongo abelii retro_pabe_2266

Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000149541 1 retrocopy
retro_hsap_2724 ,
Gorilla gorilla ENSGGOG000000136041 retrocopy
Nomascus leucogenys ENSNLEG000000039561 retrocopy
Pongo abelii ENSPPYG000000259071 retrocopy
Pan troglodytes ENSPTRG000000396651 retrocopy

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 = 0.24 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .12 RPM
FIN_HG00377 0 .20 RPM
FIN_HG00378 0 .08 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .11 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .16 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .20 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .16 RPM


Indel association:

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




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