RetrogeneDB ID:

retro_hsap_3240

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:132284184..132284407(+)
Located in intron of:ENSG00000072364
Retrocopy
information
Ensembl ID:ENSG00000225364
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP6V0E1
Ensembl ID:ENSG00000113732
Aliases:None
Description:ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1 [Source:HGNC Symbol;Acc:863]


Retrocopy-Parental alignment summary:






>retro_hsap_3240
TATCATGGCCTCACAGTGACGAGCATGTTCTGGGGCTTTGTTGGCTTCTTTGTGCCCTAGTTCGTCACTAAGCGGCCTAA
CTGGGGAGTTATCATCACCATGATGGTGACCTGTTCAGTTTGCCACTCTCTTTTGGCTGATTGCAATTTTGGCCCAATGC
AACCCTCTCTATAGACCATGACTGAAAGATGAAACCACCTGGTATCTGAAGCATCATTGGCCT

ORF - retro_hsap_3240 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.25 %
Parental protein coverage: 97.53 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYHGLTVPLIVMSVFWGFVGFLVPWFIPKGPNRGVIITMLVTCSVCCY-LFWLIAILAQLNPLFGPQLKNE
YHGLT....V.S.FWGFVGF.VP.F..K.PN.GVIITM.VTCSV.C..LFWLIAILAQ.NPL..P.LK.E
RetrocopyYHGLT----VTSMFWGFVGFFVP*FVTKRPNWGVIITMMVTCSV-CH>LFWLIAILAQCNPLYRP*LKDE
ParentalTIWYLKYHWP
T.WYLK.HWP
RetrocopyTTWYLKHHWP

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 120 .74 RPM
bodymap2_adrenal 0 .33 RPM 143 .04 RPM
bodymap2_brain 0 .00 RPM 43 .60 RPM
bodymap2_breast 0 .00 RPM 128 .89 RPM
bodymap2_colon 0 .00 RPM 127 .06 RPM
bodymap2_heart 0 .04 RPM 71 .20 RPM
bodymap2_kidney 0 .10 RPM 168 .32 RPM
bodymap2_liver 0 .00 RPM 86 .84 RPM
bodymap2_lung 0 .00 RPM 135 .06 RPM
bodymap2_lymph_node 0 .00 RPM 146 .45 RPM
bodymap2_ovary 0 .06 RPM 121 .96 RPM
bodymap2_prostate 0 .00 RPM 136 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 49 .74 RPM
bodymap2_testis 0 .13 RPM 112 .70 RPM
bodymap2_thyroid 0 .08 RPM 176 .58 RPM
bodymap2_white_blood_cells 0 .00 RPM 213 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3240 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3240 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3240 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3240 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3240 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2190
Gorilla gorilla retro_ggor_2206
Pongo abelii retro_pabe_2688
Callithrix jacchus retro_cjac_1923
Parental genes homology:
Parental genes homology involve 23 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000151831 retrocopy
retro_acar_192,
Ailuropoda melanoleuca ENSAMEG000000112831 retrocopy
retro_amel_1124,
Bos taurus ENSBTAG000000151004 retrocopies
retro_btau_1320, retro_btau_1428, retro_btau_369, retro_btau_653,
Canis familiaris ENSCAFG000000318983 retrocopies
retro_cfam_1530, retro_cfam_1961, retro_cfam_1996,
Choloepus hoffmanni ENSCHOG000000044219 retrocopies
retro_chof_1269, retro_chof_1600, retro_chof_1795, retro_chof_1856, retro_chof_2141, retro_chof_2270, retro_chof_2440, retro_chof_718, retro_chof_779,
Callithrix jacchus ENSCJAG000000192254 retrocopies
retro_cjac_1296, retro_cjac_1616, retro_cjac_1923, retro_cjac_2873,
Felis catus ENSFCAG000000317891 retrocopy
retro_fcat_1282,
Homo sapiens ENSG00000113732 3 retrocopies
retro_hsap_2090, retro_hsap_2780, retro_hsap_3240 ,
Gorilla gorilla ENSGGOG000000067013 retrocopies
retro_ggor_1632, retro_ggor_1937, retro_ggor_2206,
Macropus eugenii ENSMEUG000000085893 retrocopies
retro_meug_1213, retro_meug_1393, retro_meug_530,
Myotis lucifugus ENSMLUG000000098042 retrocopies
retro_mluc_1749, retro_mluc_628,
Macaca mulatta ENSMMUG000000138252 retrocopies
retro_mmul_1446, retro_mmul_983,
Oryctolagus cuniculus ENSOCUG000000061742 retrocopies
retro_ocun_1653, retro_ocun_732,
Otolemur garnettii ENSOGAG000000170712 retrocopies
retro_ogar_1368, retro_ogar_529,
Ochotona princeps ENSOPRG000000006731 retrocopy
retro_opri_1191,
Pongo abelii ENSPPYG000000296693 retrocopies
retro_pabe_2006, retro_pabe_2236, retro_pabe_2688,
Pan troglodytes ENSPTRG000000175383 retrocopies
retro_ptro_1537, retro_ptro_1881, retro_ptro_2190,
Rattus norvegicus ENSRNOG000000032691 retrocopy
retro_rnor_1498,
Sarcophilus harrisii ENSSHAG000000070471 retrocopy
retro_shar_556,
Tupaia belangeri ENSTBEG000000054621 retrocopy
retro_tbel_3475,
Tarsius syrichta ENSTSYG000000065905 retrocopies
retro_tsyr_1387, retro_tsyr_1422, retro_tsyr_1971, retro_tsyr_2020, retro_tsyr_547,
Tursiops truncatus ENSTTRG000000106265 retrocopies
retro_ttru_1411, retro_ttru_1656, retro_ttru_1891, retro_ttru_250, retro_ttru_365,
Vicugna pacos ENSVPAG000000119961 retrocopy
retro_vpac_622,

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 = 0.11 RPM Legend:


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

Indel association:

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



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