RetrogeneDB ID:

retro_hsap_912

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:92069203..92069662(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235547
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFB11
Ensembl ID:ENSG00000147123
Aliases:NDUFB11, CI-ESSS, ESSS, NP17.3, Np15, P17.3
Description:NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa [Source:HGNC Symbol;Acc:20372]


Retrocopy-Parental alignment summary:






>retro_hsap_912
ATGGCAGTTGGGCTGTTAAGTTTGAGCGCTCCCAGTCTTTTGGCGGCAGTGGTGATGCAAAGGCTCTTGGCCACCCACCT
CCGCTGGGAATCCAGCTTCTCCAGGACTGTGGTCGCCCTGTCTGCTGTGGTGGGAAAACAGCCCCCGGAACTGACCGTAC
ATTGGCAGGAGGACCCAGATCCTGAGGACAAAAACTTCTATGAGAAGAACCCAGACTCCCATTGCTATGACAAGGACCCC
ATTTTGGACATCTGGAACATGTGAGTTGTCTTCTTCTTTGGCGTCTCCATTGTCCCGGTCCTTGGCAGCACCTTTGTGGC
CTATCTGCCTGATTACAGGATGCGAGAGTGGGCCCACTGCAGAGCTGAGATGCTTGTGAAATACCGAGAGGCCAAAGACC
TTCCCATCATGGAATCCAACTGCTTCAACCCCAGCACGATCCAGTTGCCAGAGGATGAG

ORF - retro_hsap_912 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.86 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAGLFGLSARRLLAAAATRGLPAARVRWESSFSRTVVAPSAVAGKRPPEPTTPWQEDPEPEDENLYEKN
MA.GL..LSA..LLAA.....L.A...RWESSFSRTVVA.SAV.GK.PPE.T..WQEDP.PED.N.YEKN
RetrocopyMAVGLLSLSAPSLLAAVVMQRLLATHLRWESSFSRTVVALSAVVGKQPPELTVHWQEDPDPEDKNFYEKN
ParentalPDSHGYDKDPVLDVWNMRLVFFFGVSIILVLGSTFVAYLPDYRMKEWSRREAERLVKYREANGLPIMESN
PDSH.YDKDP.LD.WNM..VFFFGVSI..VLGSTFVAYLPDYRM.EW....AE.LVKYREA..LPIMESN
RetrocopyPDSHCYDKDPILDIWNM*VVFFFGVSIVPVLGSTFVAYLPDYRMREWAHCRAEMLVKYREAKDLPIMESN
ParentalCFDPSKIQLPEDE
CF.PS.IQLPEDE
RetrocopyCFNPSTIQLPEDE

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 14 .61 RPM
bodymap2_adrenal 0 .00 RPM 27 .37 RPM
bodymap2_brain 0 .02 RPM 19 .22 RPM
bodymap2_breast 0 .00 RPM 17 .74 RPM
bodymap2_colon 0 .00 RPM 21 .87 RPM
bodymap2_heart 0 .00 RPM 37 .79 RPM
bodymap2_kidney 0 .00 RPM 24 .01 RPM
bodymap2_liver 0 .00 RPM 35 .74 RPM
bodymap2_lung 0 .00 RPM 21 .01 RPM
bodymap2_lymph_node 0 .00 RPM 28 .31 RPM
bodymap2_ovary 0 .00 RPM 14 .17 RPM
bodymap2_prostate 0 .00 RPM 24 .04 RPM
bodymap2_skeletal_muscle 0 .00 RPM 49 .58 RPM
bodymap2_testis 0 .00 RPM 14 .52 RPM
bodymap2_thyroid 0 .00 RPM 36 .74 RPM
bodymap2_white_blood_cells 0 .00 RPM 25 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_912 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_912 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_912 retrocopy 5' end.

Lab - click to see more details

retro_hsap_912 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_912 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_633
Pongo abelii retro_pabe_788
Macaca mulatta retro_mmul_1116
Parental genes homology:
Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000147123 1 retrocopy
retro_hsap_912 ,
Macaca mulatta ENSMMUG000000174222 retrocopies
retro_mmul_1116, retro_mmul_830,
Monodelphis domestica ENSMODG000000184911 retrocopy
retro_mdom_1063,
Mus musculus ENSMUSG000000310592 retrocopies
retro_mmus_245, retro_mmus_2602,
Pongo abelii ENSPPYG000000202841 retrocopy
retro_pabe_788,
Pan troglodytes ENSPTRG000000218361 retrocopy
retro_ptro_633,
Rattus norvegicus ENSRNOG000000083291 retrocopy
retro_rnor_151,
Ictidomys tridecemlineatus ENSSTOG000000268211 retrocopy
retro_itri_1084,

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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