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






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 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

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_748 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_748 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_748 retrocopy 5' end.

Lab - click to see more details

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
retro_amel_1930, retro_amel_292, retro_amel_84,
Canis familiaris ENSCAFG000000192542 retrocopies
retro_cfam_185, retro_cfam_42,
Callithrix jacchus ENSCJAG000000109573 retrocopies
retro_cjac_1640, retro_cjac_2335, retro_cjac_37,
Cavia porcellus ENSCPOG000000022382 retrocopies
retro_cpor_83, retro_cpor_909,
Homo sapiens ENSG00000160075 8 retrocopies
retro_hsap_3778, retro_hsap_4741, retro_hsap_747, retro_hsap_748 , retro_hsap_749, retro_hsap_841, retro_hsap_842, retro_hsap_843,
Gorilla gorilla ENSGGOG000000044211 retrocopy
retro_ggor_206,
Loxodonta africana ENSLAFG000000020764 retrocopies
retro_lafr_1153, retro_lafr_1154, retro_lafr_1155, retro_lafr_400,
Macropus eugenii ENSMEUG000000151701 retrocopy
retro_meug_1253,
Myotis lucifugus ENSMLUG000000165172 retrocopies
retro_mluc_292, retro_mluc_371,
Macaca mulatta ENSMMUG000000015511 retrocopy
retro_mmul_159,
Monodelphis domestica ENSMODG000000066163 retrocopies
retro_mdom_16, retro_mdom_1997, retro_mdom_487,
Mustela putorius furoENSMPUG000000143942 retrocopies
retro_mputfur_108, retro_mputfur_1408,
Mus musculus ENSMUSG000000290381 retrocopy
retro_mmus_1317,
Otolemur garnettii ENSOGAG000000244302 retrocopies
retro_ogar_124, retro_ogar_13,
Pongo abelii ENSPPYG000000020001 retrocopy
retro_pabe_53,
Pan troglodytes ENSPTRG0000000003416 retrocopies
retro_ptro_2560, retro_ptro_2963, retro_ptro_3016, retro_ptro_3017, retro_ptro_3018, retro_ptro_3019, retro_ptro_3020, retro_ptro_3021, retro_ptro_3022, retro_ptro_3023, retro_ptro_3024, retro_ptro_3025, retro_ptro_3026, retro_ptro_3156, retro_ptro_531, retro_ptro_532,
Pteropus vampyrus ENSPVAG000000176954 retrocopies
retro_pvam_11, retro_pvam_1151, retro_pvam_272, retro_pvam_767,
Rattus norvegicus ENSRNOG000000178292 retrocopies
retro_rnor_1169, retro_rnor_2766,
Sus scrofa ENSSSCG000000033482 retrocopies
retro_sscr_1179, retro_sscr_38,
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
retro_itri_1055, retro_itri_1352, retro_itri_1496, retro_itri_99,
Tursiops truncatus ENSTTRG000000170512 retrocopies
retro_ttru_1264, retro_ttru_1265,

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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