RetrogeneDB ID:

retro_hsap_4103

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:103254265..103254419(-)
Located in intron of:ENSG00000246263
Retrocopy
information
Ensembl ID:ENSG00000253328
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SUMO3
Ensembl ID:ENSG00000184900
Aliases:SUMO3, SMT3A, SMT3H1, SUMO-3, Smt3B
Description:small ubiquitin-like modifier 3 [Source:HGNC Symbol;Acc:11124]


Retrocopy-Parental alignment summary:






>retro_hsap_4103
CCACTTAGTAAATTAATGAAAGCCTATTGTGAACAGGGTTAGGCAATGAGGTTGATCAGATTCTAGACTTCATGTGCAAC
CAATCAATGAAATAGACACACCTGTAAAGTTGAAGATGGAGGCTAAAGATACAATTAATGTGTTCCAAGGACAG

ORF - retro_hsap_4103 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.81 %
Parental protein coverage: 50.49 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPLSKLMKAYCERQGLSMRQIRF-RFDGQPINETDTPAQLEMEDEDTIDVFQQQ
PLSKLMKAYCE.QG..MR.IRF.R...QPINE.DTP..L.ME..DTI.VFQ.Q
RetrocopyPLSKLMKAYCE-QG*AMRLIRF>RLHVQPINEIDTPVKLKMEAKDTINVFQGQ

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 .02 RPM 73 .09 RPM
bodymap2_adrenal 0 .49 RPM 115 .41 RPM
bodymap2_brain 0 .05 RPM 93 .20 RPM
bodymap2_breast 0 .00 RPM 71 .36 RPM
bodymap2_colon 0 .00 RPM 64 .00 RPM
bodymap2_heart 0 .00 RPM 65 .74 RPM
bodymap2_kidney 0 .00 RPM 70 .67 RPM
bodymap2_liver 0 .13 RPM 47 .08 RPM
bodymap2_lung 0 .26 RPM 93 .79 RPM
bodymap2_lymph_node 0 .13 RPM 74 .26 RPM
bodymap2_ovary 0 .02 RPM 93 .24 RPM
bodymap2_prostate 0 .16 RPM 72 .36 RPM
bodymap2_skeletal_muscle 0 .00 RPM 42 .16 RPM
bodymap2_testis 0 .28 RPM 94 .32 RPM
bodymap2_thyroid 0 .24 RPM 121 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 92 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4103 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4103 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4103 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4103 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4103 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 108 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000173213 retrocopies
retro_btau_1730, retro_btau_580, retro_btau_701,
Bos taurus ENSBTAG000000301698 retrocopies
retro_btau_1047, retro_btau_1484, retro_btau_1804, retro_btau_260, retro_btau_344, retro_btau_489, retro_btau_582, retro_btau_895,
Callithrix jacchus ENSCJAG0000001052920 retrocopies
retro_cjac_1110, retro_cjac_1128, retro_cjac_1525, retro_cjac_1752, retro_cjac_1938, retro_cjac_1957, retro_cjac_1993, retro_cjac_2460, retro_cjac_2481, retro_cjac_2616, retro_cjac_2651, retro_cjac_2886, retro_cjac_2899, retro_cjac_2985, retro_cjac_3088, retro_cjac_3137, retro_cjac_4123, retro_cjac_711, retro_cjac_771, retro_cjac_774,
Cavia porcellus ENSCPOG000000252033 retrocopies
retro_cpor_328, retro_cpor_645, retro_cpor_963,
Felis catus ENSFCAG000000265504 retrocopies
retro_fcat_1210, retro_fcat_1947, retro_fcat_823, retro_fcat_836,
Homo sapiens ENSG000001160305 retrocopies
retro_hsap_2007, retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Homo sapiens ENSG00000184900 4 retrocopies
retro_hsap_1675, retro_hsap_1841, retro_hsap_3672, retro_hsap_4103 ,
Homo sapiens ENSG000001886122 retrocopies
retro_hsap_4036, retro_hsap_4095,
Myotis lucifugus ENSMLUG000000253424 retrocopies
retro_mluc_1502, retro_mluc_272, retro_mluc_340, retro_mluc_625,
Myotis lucifugus ENSMLUG000000286012 retrocopies
retro_mluc_1321, retro_mluc_2494,
Macaca mulatta ENSMMUG000000067603 retrocopies
retro_mmul_2131, retro_mmul_2215, retro_mmul_47,
Mustela putorius furoENSMPUG000000102341 retrocopy
retro_mputfur_1504,
Mustela putorius furoENSMPUG000000139549 retrocopies
retro_mputfur_1086, retro_mputfur_1403, retro_mputfur_1535, retro_mputfur_273, retro_mputfur_275, retro_mputfur_385, retro_mputfur_666, retro_mputfur_948, retro_mputfur_995,
Mus musculus ENSMUSG000000202651 retrocopy
retro_mmus_3548,
Nomascus leucogenys ENSNLEG000000023519 retrocopies
retro_nleu_1084, retro_nleu_1253, retro_nleu_1736, retro_nleu_2052, retro_nleu_21, retro_nleu_2128, retro_nleu_3039, retro_nleu_523, retro_nleu_572,
Oryctolagus cuniculus ENSOCUG000000217394 retrocopies
retro_ocun_1024, retro_ocun_1631, retro_ocun_1690, retro_ocun_321,
Otolemur garnettii ENSOGAG0000000471510 retrocopies
retro_ogar_1199, retro_ogar_1646, retro_ogar_1945, retro_ogar_2958, retro_ogar_328, retro_ogar_3469, retro_ogar_371, retro_ogar_419, retro_ogar_526, retro_ogar_967,
Rattus norvegicus ENSRNOG000000036702 retrocopies
retro_rnor_418, retro_rnor_67,
Rattus norvegicus ENSRNOG000000384891 retrocopy
retro_rnor_2158,
Ictidomys tridecemlineatus ENSSTOG000000105872 retrocopies
retro_itri_116, retro_itri_1259,
Ictidomys tridecemlineatus ENSSTOG0000002468510 retrocopies
retro_itri_1017, retro_itri_1123, retro_itri_1355, retro_itri_202, retro_itri_264, retro_itri_272, retro_itri_79, retro_itri_921, retro_itri_981, retro_itri_983,
Takifugu rubripes ENSTRUG000000148921 retrocopy
retro_trub_25,

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 = 0.68 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .21 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .42 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .22 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .24 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 0 .33 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .22 RPM
FIN_HG00321 0 .27 RPM
FIN_HG00328 0 .21 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .21 RPM
GBR_HG00119 0 .34 RPM
GBR_HG00131 0 .32 RPM
GBR_HG00133 0 .22 RPM
GBR_HG00134 0 .44 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .22 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .19 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .41 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .29 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .68 RPM
YRI_NA18907 0 .24 RPM
YRI_NA18916 0 .19 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .27 RPM
YRI_NA19114 0 .16 RPM
YRI_NA19118 0 .19 RPM
YRI_NA19213 0 .62 RPM
YRI_NA19214 0 .12 RPM
YRI_NA19223 0 .24 RPM

Indel association:

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





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