RetrogeneDB ID:

retro_hsap_4856

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:70956306..70956506(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237182
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA4
Ensembl ID:ENSG00000189043
Aliases:NDUFA4, CI-9k, CI-MLRQ, MLRQ
Description:NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa [Source:HGNC Symbol;Acc:7687]


Retrocopy-Parental alignment summary:






>retro_hsap_4856
CTCTCTCTCTTTGTATATATGTGAGCAGGAGGCACCAGAGCAGGGCTGCATGTCTTGCATCTGGCACTGTTTAACCCAGG
TGTTAGCTGGGACAGAAAGAATCCCCCAGAACCCTGGAATAAACTGGGTCCCAATGATCAATACAAGTTCTACTCAGTGA
ATGTAGATTACAGCAAACTGAAAAAGAATGTCCAGACTTC

ORF - retro_hsap_4856 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.53 %
Parental protein coverage: 81.48 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalIPLFVFIGTGATGATLYLLRLALFNPDVCWDRNN-PEPWNKLGPNDQYKFYSVNVDYSKLKK-ERPDF
..LFV....G.T.A.L..L.LALFNP.V.WDR.N.PEPWNKLGPNDQYKFYSVNVDYSKLKK.E.PDF
RetrocopyLSLFVYM*AGGTRAGLHVLHLALFNPGVSWDRKNPPEPWNKLGPNDQYKFYSVNVDYSKLKK<ECPDF

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 56 .73 RPM
bodymap2_adrenal 0 .00 RPM 81 .49 RPM
bodymap2_brain 0 .00 RPM 204 .12 RPM
bodymap2_breast 0 .00 RPM 82 .72 RPM
bodymap2_colon 0 .00 RPM 80 .77 RPM
bodymap2_heart 0 .00 RPM 501 .83 RPM
bodymap2_kidney 0 .00 RPM 130 .35 RPM
bodymap2_liver 0 .00 RPM 110 .92 RPM
bodymap2_lung 0 .00 RPM 105 .89 RPM
bodymap2_lymph_node 0 .00 RPM 81 .06 RPM
bodymap2_ovary 0 .00 RPM 64 .00 RPM
bodymap2_prostate 0 .00 RPM 120 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 121 .57 RPM
bodymap2_testis 0 .00 RPM 80 .47 RPM
bodymap2_thyroid 0 .00 RPM 114 .85 RPM
bodymap2_white_blood_cells 0 .00 RPM 64 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4856 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4856 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4856 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4856 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4856 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 137 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000249310 retrocopies
retro_amel_1356, retro_amel_1633, retro_amel_18, retro_amel_1800, retro_amel_1866, retro_amel_533, retro_amel_608, retro_amel_638, retro_amel_845, retro_amel_955,
Choloepus hoffmanni ENSCHOG000000123301 retrocopy
retro_chof_2667,
Callithrix jacchus ENSCJAG000000007483 retrocopies
retro_cjac_3291, retro_cjac_36, retro_cjac_90,
Dasypus novemcinctus ENSDNOG0000001121712 retrocopies
retro_dnov_1874, retro_dnov_1921, retro_dnov_2015, retro_dnov_2258, retro_dnov_2566, retro_dnov_2567, retro_dnov_2641, retro_dnov_349, retro_dnov_506, retro_dnov_725, retro_dnov_744, retro_dnov_764,
Homo sapiens ENSG000001856332 retrocopies
retro_hsap_4698, retro_hsap_4857,
Homo sapiens ENSG00000189043 18 retrocopies
retro_hsap_1459, retro_hsap_200, retro_hsap_2374, retro_hsap_2386, retro_hsap_259, retro_hsap_2685, retro_hsap_2726, retro_hsap_285, retro_hsap_3241, retro_hsap_4067, retro_hsap_4188, retro_hsap_4292, retro_hsap_4699, retro_hsap_4700, retro_hsap_4750, retro_hsap_4856 , retro_hsap_650, retro_hsap_877,
Gorilla gorilla ENSGGOG000000014373 retrocopies
retro_ggor_249, retro_ggor_30, retro_ggor_567,
Microcebus murinus ENSMICG000000139995 retrocopies
retro_mmur_1225, retro_mmur_1314, retro_mmur_133, retro_mmur_341, retro_mmur_696,
Myotis lucifugus ENSMLUG000000064706 retrocopies
retro_mluc_1778, retro_mluc_1821, retro_mluc_329, retro_mluc_450, retro_mluc_517, retro_mluc_849,
Macaca mulatta ENSMMUG000000208942 retrocopies
retro_mmul_272, retro_mmul_274,
Monodelphis domestica ENSMODG000000141072 retrocopies
retro_mdom_1095, retro_mdom_1593,
Oryctolagus cuniculus ENSOCUG000000293721 retrocopy
retro_ocun_41,
Otolemur garnettii ENSOGAG0000000035817 retrocopies
retro_ogar_1023, retro_ogar_1026, retro_ogar_1319, retro_ogar_1403, retro_ogar_1566, retro_ogar_1960, retro_ogar_1976, retro_ogar_2050, retro_ogar_2350, retro_ogar_2528, retro_ogar_3023, retro_ogar_3413, retro_ogar_3434, retro_ogar_3457, retro_ogar_694, retro_ogar_731, retro_ogar_997,
Pongo abelii ENSPPYG000000177805 retrocopies
retro_pabe_2296, retro_pabe_24, retro_pabe_301, retro_pabe_3339, retro_pabe_678,
Pan troglodytes ENSPTRG0000001893419 retrocopies
retro_ptro_1134, retro_ptro_1736, retro_ptro_1745, retro_ptro_1811, retro_ptro_182, retro_ptro_1842, retro_ptro_219, retro_ptro_2191, retro_ptro_235, retro_ptro_2756, retro_ptro_2844, retro_ptro_2908, retro_ptro_3034, retro_ptro_3123, retro_ptro_3165, retro_ptro_3233, retro_ptro_473, retro_ptro_766, retro_ptro_993,
Tupaia belangeri ENSTBEG0000001662916 retrocopies
retro_tbel_1049, retro_tbel_1848, retro_tbel_2008, retro_tbel_2058, retro_tbel_2194, retro_tbel_2274, retro_tbel_2423, retro_tbel_2761, retro_tbel_3262, retro_tbel_4255, retro_tbel_4309, retro_tbel_436, retro_tbel_4380, retro_tbel_4426, retro_tbel_4719, retro_tbel_815,
Tarsius syrichta ENSTSYG0000000004115 retrocopies
retro_tsyr_1427, retro_tsyr_1650, retro_tsyr_1766, retro_tsyr_1948, retro_tsyr_1973, retro_tsyr_1974, retro_tsyr_198, retro_tsyr_270, retro_tsyr_425, retro_tsyr_473, retro_tsyr_492, retro_tsyr_659, retro_tsyr_685, retro_tsyr_821, retro_tsyr_937,

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 ) 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 .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 .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 .00 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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