RetrogeneDB ID:

retro_hsap_1662

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:4612814..4613194(-)
Located in intron of:ENSG00000205832
Retrocopy
information
Ensembl ID:ENSG00000261612
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SUB1
Ensembl ID:ENSG00000113387
Aliases:SUB1, P15, PC4, p14
Description:SUB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19985]


Retrocopy-Parental alignment summary:






>retro_hsap_1662
ATGCCTAAAGCAAAGGAACTTGTTTCTTCAAACTCTTCTGGCAGTGATTCTGACAGTGAGGTTGACAAAAACTTAAAGAG
GAAAAAGCAAGTTGCTCCAGAAAAACCTGTAAAGAAGCAAAAGACAGGCGAAACTTGGAGAGCTCTGTCATCTTCTGACA
GAGGAGCAGCAGCAGAGATGGTAACATGTTTCAGATTGGGAAAATGAGGTACGTTGGCGTTCAAGATTTTAAAGGCAAAG
TGCTAATTGATATTGGAGAATATTGGATGGATCCTGAAGGTGAAATGAAACCAGGAAGAAAAGGTATTTCTTTAAATCCA
GAACAATGGAGCCAGCTGACAGAACAGATTTCTGACACTGATGATACAGTAAGAAACCTG

ORF - retro_hsap_1662 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.28 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPKSKELVSSSSSGSDSDSEVDKKLKRKKQVAPEKPVKKQKTGETSRALSSSK-QSSSSRDDNMFQIGKM
MPK.KELVSS.SSGSDSDSEVDK.LKRKKQVAPEKPVKKQKTGET.RALSSS..Q.SSSRD.NMFQIGKM
RetrocopyMPKAKELVSSNSSGSDSDSEVDKNLKRKKQVAPEKPVKKQKTGETWRALSSSD<QRSSSRDGNMFQIGKM
ParentalRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
RYV.V.DFKGKVLIDI.EYWMDPEGEMKPGRKGISLNPEQWSQL.EQISD.DD.VR.L
RetrocopyRYVGVQDFKGKVLIDIGEYWMDPEGEMKPGRKGISLNPEQWSQLTEQISDTDDTVRNL

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 .04 RPM 97 .38 RPM
bodymap2_adrenal 0 .10 RPM 167 .50 RPM
bodymap2_brain 0 .05 RPM 239 .91 RPM
bodymap2_breast 0 .04 RPM 243 .76 RPM
bodymap2_colon 0 .06 RPM 165 .36 RPM
bodymap2_heart 0 .00 RPM 103 .86 RPM
bodymap2_kidney 0 .00 RPM 139 .08 RPM
bodymap2_liver 0 .00 RPM 62 .80 RPM
bodymap2_lung 0 .00 RPM 162 .62 RPM
bodymap2_lymph_node 0 .00 RPM 142 .59 RPM
bodymap2_ovary 0 .00 RPM 126 .48 RPM
bodymap2_prostate 0 .02 RPM 113 .45 RPM
bodymap2_skeletal_muscle 0 .02 RPM 52 .31 RPM
bodymap2_testis 0 .04 RPM 179 .58 RPM
bodymap2_thyroid 0 .00 RPM 138 .58 RPM
bodymap2_white_blood_cells 0 .02 RPM 157 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1662 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1662 retrocopy.

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_51611242 libraries272 libraries1056 libraries197 libraries62 libraries

The graphical summary, for retro_hsap_1662 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_1662 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1662 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1254
Pongo abelii retro_pabe_1371
Parental genes homology:
Parental genes homology involve 20 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000188795 retrocopies
retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus ENSCJAG000000187182 retrocopies
retro_cjac_1908, retro_cjac_484,
Cavia porcellus ENSCPOG000000055844 retrocopies
retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus ENSDNOG000000076115 retrocopies
retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Homo sapiens ENSG00000113387 2 retrocopies
retro_hsap_1662 , retro_hsap_3934,
Gorilla gorilla ENSGGOG000000270333 retrocopies
retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana ENSLAFG000000110061 retrocopy
retro_lafr_19,
Macropus eugenii ENSMEUG000000077704 retrocopies
retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus ENSMICG000000145352 retrocopies
retro_mmur_1115, retro_mmur_17,
Myotis lucifugus ENSMLUG000000136856 retrocopies
retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta ENSMMUG000000114702 retrocopies
retro_mmul_2318, retro_mmul_993,
Monodelphis domestica ENSMODG000000204103 retrocopies
retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furoENSMPUG000000151852 retrocopies
retro_mputfur_186, retro_mputfur_295,
Mus musculus ENSMUSG000000222054 retrocopies
retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus ENSOCUG000000062625 retrocopies
retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii ENSOGAG000000090126 retrocopies
retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Pongo abelii ENSPPYG000000153792 retrocopies
retro_pabe_124, retro_pabe_1371,
Rattus norvegicus ENSRNOG0000005056312 retrocopies
retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii ENSSHAG000000149861 retrocopy
retro_shar_628,
Tarsius syrichta ENSTSYG000000140692 retrocopies
retro_tsyr_528, retro_tsyr_895,

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 = 0.28 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .28 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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