RetrogeneDB ID:

retro_hsap_748

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:4299936..4300519(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236175
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SSU72
Ensembl ID:ENSG00000160075
Aliases:SSU72, HSPC182, PNAS-120
Description:SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]


Retrocopy-Parental alignment summary:






>retro_hsap_748
ATGCTCTCCTCCACACTCAGGGTGGCTGTGGTGTGCGTGAGCAATGTCAACAGGAGCATGGAGGCCCACAGCATCCTCAG
GAGAAAAGGGCTAAGTGTCCGGTCTTTTGGAACTGAATCTCATGTGAGGCTACCAGGACCAAGACCCAATCGTCCTGTAG
TTTACGATTTTGCAACAACATATAAGGAGATGTACAATGACCTCCTCAGGAAAGATAGAGAACGCTACACCCGCAACGGA
ATCTTACACATCTTGGGAAGAAATGAGAGAATCAAGCCCGGTCCAGAAAGATTTCAGGAGTGCACTGATTTCTTTGATGT
CATCTTCACCTGTGAGGAGAGTGTCTATGACACAGTGGTGGAAGATCTGTGTTCCAGAGAACAGCAGACCTTTCAGCCTG
TGCACGTGATCAACATGGACATCCAAGATACCCTGGAAGATGCCACCCTGGGAGCTTTCCTCATCTGTGAGATTTGCCAG
TGCCTGGCAGCAGTCAGACGACATGGAAGACAATCTGGAAGAGCTGCTGTTGCAAATGGAGGAGAAGGCAGGAAAAAGCT
TTCTTCACACCGTCTGCTTCTAC

ORF - retro_hsap_748 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPSSPLRVAVVCSSNQNRSMEAHNILSKRGFSVRSFGTGTHVKLPGPAPDKPNVYDFKTTYDQMYNDLLR
M.SS.LRVAVVC.SN.NRSMEAH.IL...G.SVRSFGT..HV.LPGP.P..P.VYDF.TTY..MYNDLLR
RetrocopyMLSSTLRVAVVCVSNVNRSMEAHSILRRKGLSVRSFGTESHVRLPGPRPNRPVVYDFATTYKEMYNDLLR
ParentalKDKELYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVVNVD
KD.E.YT.NGILH.L.RN.RIKP.PERFQ.C.D.FD.I.TCEE.VYD.VVEDL.SREQ.T.QPVHV.N.D
RetrocopyKDRERYTRNGILHILGRNERIKPGPERFQECTDFFDVIFTCEESVYDTVVEDLCSREQQTFQPVHVINMD
ParentalIQDNHEEATLGAFLICELCQCI-QHTEDMENEIDELLQEFEEKSGRTFLHTVCFY
IQD..E.ATLGAFLICE.CQC..Q...DME....ELL...EEK.G..FLHTVCFY
RetrocopyIQDTLEDATLGAFLICEICQCL>QQSDDMEDNLEELLLQMEEKAGKSFLHTVCFY

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 63 .69 RPM
bodymap2_adrenal 0 .00 RPM 88 .24 RPM
bodymap2_brain 0 .00 RPM 68 .40 RPM
bodymap2_breast 0 .00 RPM 79 .01 RPM
bodymap2_colon 0 .00 RPM 63 .27 RPM
bodymap2_heart 0 .00 RPM 52 .26 RPM
bodymap2_kidney 0 .00 RPM 73 .08 RPM
bodymap2_liver 0 .00 RPM 42 .33 RPM
bodymap2_lung 0 .00 RPM 55 .63 RPM
bodymap2_lymph_node 0 .00 RPM 91 .51 RPM
bodymap2_ovary 0 .00 RPM 93 .07 RPM
bodymap2_prostate 0 .00 RPM 73 .70 RPM
bodymap2_skeletal_muscle 0 .00 RPM 107 .38 RPM
bodymap2_testis 0 .00 RPM 67 .93 RPM
bodymap2_thyroid 0 .00 RPM 118 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 89 .23 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_748 was not detected
No EST(s) were mapped for retro_hsap_748 retrocopy.
No TSS is located nearby retro_hsap_748 retrocopy 5' end.
retro_hsap_748 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_748 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137363 retrocopies
Canis familiaris ENSCAFG000000192542 retrocopies
Callithrix jacchus ENSCJAG000000109573 retrocopies
Cavia porcellus ENSCPOG000000022382 retrocopies
Homo sapiens ENSG00000160075 8 retrocopies
Gorilla gorilla ENSGGOG000000044211 retrocopy
Loxodonta africana ENSLAFG000000020764 retrocopies
Macropus eugenii ENSMEUG000000151701 retrocopy
Myotis lucifugus ENSMLUG000000165172 retrocopies
Macaca mulatta ENSMMUG000000015511 retrocopy
Monodelphis domestica ENSMODG000000066163 retrocopies
Mustela putorius furoENSMPUG000000143942 retrocopies
Mus musculus ENSMUSG000000290381 retrocopy
Otolemur garnettii ENSOGAG000000244302 retrocopies
Pongo abelii ENSPPYG000000020001 retrocopy
Pan troglodytes ENSPTRG0000000003416 retrocopies
Pteropus vampyrus ENSPVAG000000176954 retrocopies
Rattus norvegicus ENSRNOG000000178292 retrocopies
Sus scrofa ENSSSCG000000033482 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
Tursiops truncatus ENSTTRG000000170512 retrocopies

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 ) 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 .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 .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 .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:

The presence of retro_hsap_748 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_748 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 11:4272152..4327520 97.54 94.89 98.97 92.42 97.27 96.67 98.82 100 97.75 93.01 97.96 90.45 86.08 85.5


Indel #1, located at the genomic coordinates 11:4272152..4327520.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 92.42 % Puerto Ricansfrom Puerto Rico PUR 97.27 % Colombians fromMedellin, Colombia CLM 96.67 % Americans of AfricanAncestry in SW USA ASW 97.54 % Yoruba in Ibadan,Nigeria YRI 94.89 % Luhya in Webuye,Kenya LWK 98.97 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 98.82 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 97.75 % Finnish in Finland FIN 93.01 % Toscani in Italia TSI 97.96 % Han Chinese in Bejing,China CHB 86.08 % Japanese in Tokyo,Japan 90.45 % Southern Han Chinese CHS 85.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA





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