RetrogeneDB ID:

retro_hsap_311

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:223119009..223119239(+)
Located in intron of:ENSG00000154309
Retrocopy
information
Ensembl ID:ENSG00000234523
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFB1
Ensembl ID:ENSG00000183648
Aliases:None
Description:NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa [Source:HGNC Symbol;Acc:7695]


Retrocopy-Parental alignment summary:






>retro_hsap_311
GAGCTCATCACTACCCTTGGTTGTGGGGTCATTGTTGGAACTGGGGCTTTTGCAATCATGGTGGACTGACTTGAGACTGT
GTATGAGCACTGGGTCCATAGACTTGTCCGTATAGGATTTGTCTTTGTATGTTATCTAAAGAGAAAGAATGATGAAAAGC
TAACTGCCTTCTGGAAAAATAGTATTTTATTTAAAAGGGAATTGACACCCATGGAGAAGTTGCTTGGAAG

ORF - retro_hsap_311 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.26 %
Parental protein coverage: 73.33 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEFPVALGLGVAVGAEAAAIMVNLLQIVRDHWVHVLVPMGFVIGCYLDRKSDERLTAFRNKSMLFKRELQP
E....LG.GV.VG..A.AIMV..L..V..HWVH.LV..GFV..CYL.RK.DE.LTAF...S.LFKREL.P
RetrocopyELITTLGCGVIVGTGAFAIMVD*LETVYEHWVHRLVRIGFVFVCYLKRKNDEKLTAFWKNSILFKRELTP
ParentalSE-EVTWK
.E.EV.WK
RetrocopyME<EVAWK

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 12 .88 RPM
bodymap2_adrenal 0 .00 RPM 28 .58 RPM
bodymap2_brain 0 .00 RPM 19 .48 RPM
bodymap2_breast 0 .04 RPM 19 .42 RPM
bodymap2_colon 0 .12 RPM 28 .31 RPM
bodymap2_heart 0 .04 RPM 93 .97 RPM
bodymap2_kidney 0 .12 RPM 34 .50 RPM
bodymap2_liver 0 .04 RPM 43 .26 RPM
bodymap2_lung 0 .11 RPM 34 .74 RPM
bodymap2_lymph_node 0 .13 RPM 35 .18 RPM
bodymap2_ovary 0 .08 RPM 11 .78 RPM
bodymap2_prostate 0 .26 RPM 42 .88 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .59 RPM
bodymap2_testis 0 .08 RPM 17 .95 RPM
bodymap2_thyroid 0 .13 RPM 19 .58 RPM
bodymap2_white_blood_cells 0 .00 RPM 37 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_311 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_311 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_311 retrocopy 5' end.

Lab - click to see more details

retro_hsap_311 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_311 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_253
Macaca mulatta retro_mmul_538
Parental genes homology:
Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000148371 retrocopy
retro_amel_1060,
Callithrix jacchus ENSCJAG000000180675 retrocopies
retro_cjac_1027, retro_cjac_1053, retro_cjac_1330, retro_cjac_2586, retro_cjac_3294,
Homo sapiens ENSG00000183648 2 retrocopies
retro_hsap_2646, retro_hsap_311 ,
Macaca mulatta ENSMMUG000000224282 retrocopies
retro_mmul_1520, retro_mmul_538,
Nomascus leucogenys ENSNLEG000000171291 retrocopy
retro_nleu_652,
Ochotona princeps ENSOPRG000000127312 retrocopies
retro_opri_22, retro_opri_992,
Pongo abelii ENSPPYG000000060761 retrocopy
retro_pabe_2325,
Pan troglodytes ENSPTRG000000066492 retrocopies
retro_ptro_1782, retro_ptro_253,
Pteropus vampyrus ENSPVAG000000153191 retrocopy
retro_pvam_642,
Tursiops truncatus ENSTTRG000000081302 retrocopies
retro_ttru_1515, retro_ttru_830,
Vicugna pacos ENSVPAG000000035022 retrocopies
retro_vpac_257, retro_vpac_39,

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 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 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 .02 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 .02 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 .02 RPM
TSI_NA20518 0 .06 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 .07 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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