RetrogeneDB ID:

retro_hsap_3029

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:24659729..24659997(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000249256
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5L
Ensembl ID:ENSG00000167283
Aliases:ATP5L, ATP5JG
Description:ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G [Source:HGNC Symbol;Acc:14247]


Retrocopy-Parental alignment summary:






>retro_hsap_3029
ATAGCCCAATTTGTCTGTAACTTTGCAGAAAAGGCCCGGGCACTGGTGAACGCTGCTGTGACTTATGCAAAGCCTGGATT
GGCCACATTTTGGTACTACGCCAAGGTTGAGCTGGTTCCTCCCACCCCTGTTGAGATTCCCTAGAGCTAGTCAGAGCCTG
AAAACAATAGTCAATAGTGCTCAGACTGGTAGCTTCAAACAGCTCACAGTTAAGGAAGCTGTGCTGAATGGTTTCGTGGT
CGCTGAGGTGTGGATGTGGTTTTGTGTT

ORF - retro_hsap_3029 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.11 %
Parental protein coverage: 86.41 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAQFVRNLVEKTPALVNAAVTYSKPRLATFWYYAKVELVPPTPAEI-PRAIQSLKKIVNSAQTGSFKQLT
.AQFV.N..EK..ALVNAAVTY.KP.LATFWYYAKVELVPPTP.EI.PRA.QSLK.IVNSAQTGSFKQLT
RetrocopyIAQFVCNFAEKARALVNAAVTYAKPGLATFWYYAKVELVPPTPVEI>PRASQSLKTIVNSAQTGSFKQLT
ParentalVKEAVLNGLVATEVLMWFYV
VKEAVLNG.V..EV.MWF.V
RetrocopyVKEAVLNGFVVAEVWMWFCV

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 42 .34 RPM
bodymap2_adrenal 0 .00 RPM 83 .37 RPM
bodymap2_brain 0 .00 RPM 72 .78 RPM
bodymap2_breast 0 .00 RPM 76 .97 RPM
bodymap2_colon 0 .00 RPM 100 .14 RPM
bodymap2_heart 0 .00 RPM 159 .67 RPM
bodymap2_kidney 0 .00 RPM 113 .93 RPM
bodymap2_liver 0 .00 RPM 91 .38 RPM
bodymap2_lung 0 .00 RPM 105 .12 RPM
bodymap2_lymph_node 0 .00 RPM 102 .50 RPM
bodymap2_ovary 0 .00 RPM 77 .78 RPM
bodymap2_prostate 0 .00 RPM 132 .71 RPM
bodymap2_skeletal_muscle 0 .00 RPM 75 .70 RPM
bodymap2_testis 0 .04 RPM 73 .64 RPM
bodymap2_thyroid 0 .00 RPM 92 .61 RPM
bodymap2_white_blood_cells 0 .00 RPM 137 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3029 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3029 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_1430991302 libraries498 libraries28 libraries1 library0 libraries

The graphical summary, for retro_hsap_3029 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_3029 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3029 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2043
Pongo abelii retro_pabe_2508
Parental genes homology:
Parental genes homology involve 27 parental genes, and 134 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000073322 retrocopies
retro_btau_105, retro_btau_245,
Choloepus hoffmanni ENSCHOG000000105893 retrocopies
retro_chof_1454, retro_chof_1865, retro_chof_2204,
Callithrix jacchus ENSCJAG000000132811 retrocopy
retro_cjac_283,
Dasypus novemcinctus ENSDNOG000000193545 retrocopies
retro_dnov_1491, retro_dnov_1872, retro_dnov_2169, retro_dnov_2341, retro_dnov_344,
Equus caballus ENSECAG000000237151 retrocopy
retro_ecab_434,
Erinaceus europaeus ENSEEUG000000098637 retrocopies
retro_eeur_106, retro_eeur_111, retro_eeur_333, retro_eeur_495, retro_eeur_499, retro_eeur_589, retro_eeur_606,
Echinops telfairi ENSETEG0000000875511 retrocopies
retro_etel_1239, retro_etel_166, retro_etel_1884, retro_etel_1885, retro_etel_2183, retro_etel_241, retro_etel_254, retro_etel_355, retro_etel_822, retro_etel_876, retro_etel_995,
Felis catus ENSFCAG000000117824 retrocopies
retro_fcat_1358, retro_fcat_1615, retro_fcat_1941, retro_fcat_371,
Homo sapiens ENSG00000167283 5 retrocopies
retro_hsap_3029 , retro_hsap_3110, retro_hsap_63, retro_hsap_860, retro_hsap_883,
Loxodonta africana ENSLAFG000000302743 retrocopies
retro_lafr_1209, retro_lafr_135, retro_lafr_3,
Macropus eugenii ENSMEUG000000152811 retrocopy
retro_meug_1774,
Microcebus murinus ENSMICG000000152336 retrocopies
retro_mmur_1428, retro_mmur_237, retro_mmur_365, retro_mmur_513, retro_mmur_700, retro_mmur_725,
Myotis lucifugus ENSMLUG000000140803 retrocopies
retro_mluc_2299, retro_mluc_2593, retro_mluc_733,
Macaca mulatta ENSMMUG000000176044 retrocopies
retro_mmul_1333, retro_mmul_22, retro_mmul_25, retro_mmul_262,
Mustela putorius furoENSMPUG000000046224 retrocopies
retro_mputfur_1036, retro_mputfur_1350, retro_mputfur_1486, retro_mputfur_966,
Mus musculus ENSMUSG000000387171 retrocopy
retro_mmus_139,
Nomascus leucogenys ENSNLEG000000073626 retrocopies
retro_nleu_425, retro_nleu_608, retro_nleu_765, retro_nleu_81, retro_nleu_841, retro_nleu_846,
Oryctolagus cuniculus ENSOCUG000000294554 retrocopies
retro_ocun_1140, retro_ocun_1156, retro_ocun_1418, retro_ocun_567,
Otolemur garnettii ENSOGAG0000001629810 retrocopies
retro_ogar_1097, retro_ogar_1102, retro_ogar_176, retro_ogar_3286, retro_ogar_3332, retro_ogar_352, retro_ogar_433, retro_ogar_444, retro_ogar_533, retro_ogar_573,
Pongo abelii ENSPPYG000000039335 retrocopies
retro_pabe_1913, retro_pabe_2508, retro_pabe_2568, retro_pabe_2589, retro_pabe_688,
Pan troglodytes ENSPTRG000000043425 retrocopies
retro_ptro_1518, retro_ptro_2043, retro_ptro_2102, retro_ptro_2478, retro_ptro_597,
Rattus norvegicus ENSRNOG0000002888419 retrocopies
retro_rnor_1145, retro_rnor_1160, retro_rnor_1185, retro_rnor_1319, retro_rnor_1345, retro_rnor_1379, retro_rnor_1420, retro_rnor_1468, retro_rnor_1993, retro_rnor_2258, retro_rnor_2271, retro_rnor_2404, retro_rnor_2573, retro_rnor_2650, retro_rnor_2723, retro_rnor_2735, retro_rnor_2929, retro_rnor_660, retro_rnor_698,
Sus scrofa ENSSSCG000000237775 retrocopies
retro_sscr_196, retro_sscr_270, retro_sscr_378, retro_sscr_463, retro_sscr_500,
Ictidomys tridecemlineatus ENSSTOG000000144002 retrocopies
retro_itri_1649, retro_itri_332,
Tupaia belangeri ENSTBEG000000099994 retrocopies
retro_tbel_1364, retro_tbel_4005, retro_tbel_857, retro_tbel_959,
Tarsius syrichta ENSTSYG000000026864 retrocopies
retro_tsyr_1516, retro_tsyr_1688, retro_tsyr_2166, retro_tsyr_578,
Tursiops truncatus ENSTTRG000000042849 retrocopies
retro_ttru_1088, retro_ttru_1125, retro_ttru_1255, retro_ttru_1537, retro_ttru_1781, retro_ttru_541, retro_ttru_716, retro_ttru_810, retro_ttru_972,

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 = 0.03 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 .03 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 .03 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:

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



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