RetrogeneDB ID:

retro_hsap_3103

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:141235322..141235694(-)
Located in intron of:ENSG00000196951
Retrocopy
information
Ensembl ID:ENSG00000249754
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFB4
Ensembl ID:ENSG00000065518
Aliases:NDUFB4, B15, CI-B15
Description:NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa [Source:HGNC Symbol;Acc:7699]


Retrocopy-Parental alignment summary:






>retro_hsap_3103
CAGTATACTCCATCGCGACTGGCCACTCTGCCCTCAACCCTCAACCCAGCTGAATACGACATATCTCTGGAGACCCAGTG
GGCACAAGCTGAGCGATTGGCCATAAGGGCCTGGCCTAAACAGGAATACCTGCTTCAGTACAACAACCCTAACCGCCAAG
GGCTCATCCAAAATACTGCCTTGATTTGTTGGACCTATGCAAGATCAGCAAGTGTCTATCCCAATTTTAGACCCGCTCCC
AAAAACCCTCTCTTGGGAGCTCTCTGTGGAATTGGGCCCCTCTTCTTCTAGTATTATGTTTTCAAAACTGACAGGGATAG
AAAAGAAAAACTTATCCAGGAAGGAAAATTGGGCTGAACATTTAACATCTCA

ORF - retro_hsap_3103 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.97 %
Parental protein coverage: 96.12 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKYKPSSLRTLPETLDPAEYNISPETRRAQAERLAIRAQLKREYLLQYNDPNRRGLIENPALLRWAYARTI
.Y.PS.L.TLP.TL.PAEY.IS.ET..AQAERLAIRA..K.EYLLQYN.PNR.GLI.N.AL..W.YAR..
RetrocopyQYTPSRLATLPSTLNPAEYDISLETQWAQAERLAIRAWPKQEYLLQYNNPNRQGLIQNTALICWTYARSA
ParentalNVYPNFRPTPKNSLMGALCGFGPLIFIYYIIKTERDRKEKLIQEGKLDRTFHLS
.VYPNFRP.PKN.L.GALCG.GPL.F.YY..KT.RDRKEKLIQEGKL..TF..S
RetrocopySVYPNFRPAPKNPLLGALCGIGPLFF*YYVFKTDRDRKEKLIQEGKLG*TFNIS

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 54 .15 RPM
bodymap2_adrenal 0 .00 RPM 50 .68 RPM
bodymap2_brain 0 .00 RPM 41 .42 RPM
bodymap2_breast 0 .00 RPM 44 .53 RPM
bodymap2_colon 0 .00 RPM 57 .85 RPM
bodymap2_heart 0 .00 RPM 168 .03 RPM
bodymap2_kidney 0 .00 RPM 68 .10 RPM
bodymap2_liver 0 .00 RPM 58 .39 RPM
bodymap2_lung 0 .00 RPM 56 .91 RPM
bodymap2_lymph_node 0 .00 RPM 60 .01 RPM
bodymap2_ovary 0 .00 RPM 42 .25 RPM
bodymap2_prostate 0 .00 RPM 80 .73 RPM
bodymap2_skeletal_muscle 0 .00 RPM 125 .75 RPM
bodymap2_testis 0 .00 RPM 53 .13 RPM
bodymap2_thyroid 0 .00 RPM 48 .90 RPM
bodymap2_white_blood_cells 0 .00 RPM 39 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3103 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3103 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3103 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3103 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3103 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2099
Pongo abelii retro_pabe_2565
Callithrix jacchus retro_cjac_2140
Parental genes homology:
Parental genes homology involve 26 parental genes, and 76 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000114621 retrocopy
retro_acar_74,
Ailuropoda melanoleuca ENSAMEG000000047612 retrocopies
retro_amel_1289, retro_amel_1491,
Bos taurus ENSBTAG000000158922 retrocopies
retro_btau_184, retro_btau_995,
Choloepus hoffmanni ENSCHOG000000000062 retrocopies
retro_chof_188, retro_chof_777,
Callithrix jacchus ENSCJAG000000086954 retrocopies
retro_cjac_1290, retro_cjac_2140, retro_cjac_302, retro_cjac_3251,
Danio rerio ENSDARG000000193321 retrocopy
retro_drer_32,
Dasypus novemcinctus ENSDNOG000000241234 retrocopies
retro_dnov_1290, retro_dnov_1833, retro_dnov_394, retro_dnov_486,
Homo sapiens ENSG00000065518 6 retrocopies
retro_hsap_1378, retro_hsap_1729, retro_hsap_2238, retro_hsap_2656, retro_hsap_2926, retro_hsap_3103 ,
Gorilla gorilla ENSGGOG000000139232 retrocopies
retro_ggor_1853, retro_ggor_2265,
Loxodonta africana ENSLAFG000000214591 retrocopy
retro_lafr_1078,
Microcebus murinus ENSMICG000000052264 retrocopies
retro_mmur_1409, retro_mmur_1415, retro_mmur_882, retro_mmur_915,
Myotis lucifugus ENSMLUG000000279513 retrocopies
retro_mluc_1433, retro_mluc_2010, retro_mluc_489,
Macaca mulatta ENSMMUG000000015924 retrocopies
retro_mmul_1217, retro_mmul_1514, retro_mmul_1979, retro_mmul_356,
Monodelphis domestica ENSMODG000000182291 retrocopy
retro_mdom_1658,
Mustela putorius furoENSMPUG000000082721 retrocopy
retro_mputfur_81,
Mus musculus ENSMUSG000000228204 retrocopies
retro_mmus_1075, retro_mmus_1077, retro_mmus_1405, retro_mmus_1820,
Nomascus leucogenys ENSNLEG000000077064 retrocopies
retro_nleu_134, retro_nleu_2889, retro_nleu_2989, retro_nleu_762,
Otolemur garnettii ENSOGAG000000059565 retrocopies
retro_ogar_1454, retro_ogar_1917, retro_ogar_1922, retro_ogar_2874, retro_ogar_3091,
Pongo abelii ENSPPYG000000135033 retrocopies
retro_pabe_1526, retro_pabe_2500, retro_pabe_2565,
Pan troglodytes ENSPTRG000000152706 retrocopies
retro_ptro_1226, retro_ptro_1582, retro_ptro_1791, retro_ptro_1980, retro_ptro_2099, retro_ptro_947,
Rattus norvegicus ENSRNOG000000027213 retrocopies
retro_rnor_275, retro_rnor_291, retro_rnor_99,
Sorex araneus ENSSARG000000124821 retrocopy
retro_sara_600,
Ictidomys tridecemlineatus ENSSTOG000000200923 retrocopies
retro_itri_3, retro_itri_666, retro_itri_786,
Tarsius syrichta ENSTSYG000000064567 retrocopies
retro_tsyr_1062, retro_tsyr_109, retro_tsyr_1617, retro_tsyr_1635, retro_tsyr_410, retro_tsyr_627, retro_tsyr_736,
Tursiops truncatus ENSTTRG000000166581 retrocopy
retro_ttru_625,
Vicugna pacos ENSVPAG000000037741 retrocopy
retro_vpac_251,

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 .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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .02 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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