RetrogeneDB ID:

retro_hsap_1798

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:4760261..4760666(-)
Located in intron of:ENSG00000141503
Retrocopy
information
Ensembl ID:ENSG00000230201
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP6V0C
Ensembl ID:ENSG00000185883
Aliases:ATP6V0C, ATP6C, ATP6L, ATPL, VATL, VPPC, Vma3
Description:ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c [Source:HGNC Symbol;Acc:855]


Retrocopy-Parental alignment summary:






>retro_hsap_1798
TCCAACAACAGCCCCGAGTATGCTTTGGTTTTCACCATCTCGGGTGCTATGGCCACCATGGTCTCCAGTGGCCTGGGTGC
TGCCTGTGGCATGGCCAAGAATGGCACCGGCATCATGGCCATGTCTGTCATGTGGCCAGAGCTGATCCACATGAAGTCCA
TCATCCCAGTGGTCATGGCTGGTATCATCACCATCTATGGCCTAGTGGCGGCTGTCCCCCCTGCCAACTCCCTGAATGAT
GACAACAGTCTCTATAGCAGTTTCCTCCAGCTGGGCGCTGGCCTGAGTGGCCTGGCAGCCGGCTTTGCCATCGTCATCGT
GGGGGACACTGGCAAGTGTGGCACTGCCCAGCAGCCCCGACTATTTGTAGGCATGATACTGATCCTCATCTTTGCCAAGG
TGCTC

ORF - retro_hsap_1798 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.54 %
Parental protein coverage: 89.03 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSKSGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEQI-MKSIIPVVMAGIIAIYGLVV
S...PEYA..F...GA.A.MV.S.LGAA.G.AK.GTGI.AMSVM.PE.I.MKSIIPVVMAGII.IYGLV.
RetrocopySNNSPEYALVFTISGAMATMVSSGLGAACGMAKNGTGIMAMSVMWPELIHMKSIIPVVMAGIITIYGLVA
ParentalAVLIANSLNDDISLYKSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVL
AV..ANSLNDD.SLY.SFLQLGAGLS....GLAAGFAI.IVGD.G..GTAQQPRLFVGMILILIFA.VL
RetrocopyAVPPANSLNDDNSLYSSFLQLGAGLS----GLAAGFAIVIVGDTGKCGTAQQPRLFVGMILILIFAKVL

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 .08 RPM 14 .69 RPM
bodymap2_adrenal 0 .31 RPM 11 .05 RPM
bodymap2_brain 0 .26 RPM 59 .58 RPM
bodymap2_breast 0 .08 RPM 11 .98 RPM
bodymap2_colon 0 .00 RPM 13 .15 RPM
bodymap2_heart 0 .07 RPM 3 .51 RPM
bodymap2_kidney 0 .04 RPM 12 .49 RPM
bodymap2_liver 0 .00 RPM 3 .84 RPM
bodymap2_lung 0 .00 RPM 9 .07 RPM
bodymap2_lymph_node 0 .00 RPM 7 .71 RPM
bodymap2_ovary 0 .02 RPM 11 .43 RPM
bodymap2_prostate 0 .00 RPM 5 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .62 RPM
bodymap2_testis 0 .09 RPM 17 .89 RPM
bodymap2_thyroid 0 .00 RPM 19 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1798 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002DBB POLR2A 17:4761588..4761788

EST - click to see more details

No EST(s) were mapped for retro_hsap_1798 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1798 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1798 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1798 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1323
Parental genes homology:
Parental genes homology involve 15 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000264281 retrocopy
retro_btau_1638,
Homo sapiens ENSG00000185883 2 retrocopies
retro_hsap_1798 , retro_hsap_3462,
Gorilla gorilla ENSGGOG000000286002 retrocopies
retro_ggor_1323, retro_ggor_2335,
Macropus eugenii ENSMEUG000000045972 retrocopies
retro_meug_1428, retro_meug_1837,
Myotis lucifugus ENSMLUG000000267152 retrocopies
retro_mluc_2507, retro_mluc_294,
Monodelphis domestica ENSMODG000000154395 retrocopies
retro_mdom_1669, retro_mdom_1739, retro_mdom_507, retro_mdom_84, retro_mdom_982,
Mus musculus ENSMUSG000000241212 retrocopies
retro_mmus_2726, retro_mmus_2888,
Nomascus leucogenys ENSNLEG000000094162 retrocopies
retro_nleu_1692, retro_nleu_2770,
Procavia capensis ENSPCAG000000150601 retrocopy
retro_pcap_148,
Pan troglodytes ENSPTRG000000076532 retrocopies
retro_ptro_1204, retro_ptro_2346,
Rattus norvegicus ENSRNOG000000065421 retrocopy
retro_rnor_118,
Sarcophilus harrisii ENSSHAG000000142511 retrocopy
retro_shar_194,
Ictidomys tridecemlineatus ENSSTOG000000134203 retrocopies
retro_itri_119, retro_itri_387, retro_itri_691,
Drosophila melanogaster FBgn02627363 retrocopies
retro_dmel_3, retro_dmel_38, retro_dmel_65,
Caenorhabditis elegans R10E11.22 retrocopies
retro_cele_1, retro_cele_5,

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 = 0.07 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 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 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 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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





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