RetrogeneDB ID:

retro_hsap_770

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:34731156..34731708(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000271369
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFB8
Ensembl ID:ENSG00000166136
Aliases:NDUFB8, ASHI, CI-ASHI
Description:NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa [Source:HGNC Symbol;Acc:7703]


Retrocopy-Parental alignment summary:






>retro_hsap_770
GTAGCCAGGGCAGGGGTCCTGGGAATCTAGTGGCTACAAAGGGCAACCCAGAATGTGGTGTCATTGAGTGCATGGCCATC
CTTCCACATGATCAAGGACATGCCCCTGGGGTTCTATTCCAAGACCCCAGAAGAATGGGCCACCGCTGCCAAGAAGTATA
ATATGTGTGTGGAAGACTATCAGCCTTACTTGGATGATGGCATGGAGTATGGTAACTACTCAAAGTTCTTTGACCATTCA
CAGTAGGAGAGGGATCTGTGGTTTGACTGGGACCACCAAGACTTGAGGTTGAACTGGGGTGAACTGATACACTGGCATCT
GGACAAGTATATCAGGAACCATGTGGATATGGCCCTCCACCCCTGTTTCTTGGAATATCATGTTCAATAATCTCTTCAGC
TTCCTGACCTTCATGAACTTTATGTTCTATGTAGTGGAGAATTATTCTACCTACCAGCCTGTGGGGCCAAAGCAGTATCC
TTTTAATAATCTGTACTTGGGACAAGACAGTGATCCACCAAAGAACCTGAGCTAGTGTTTCACTATGAGATC

ORF - retro_hsap_770 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.44 %
Parental protein coverage: 98.92 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVARAGVLGVQWLQRASRNVMPLGARTASHMTKDMFPGPYPRTPEERAAAAKKYNMRVEDYEPYPDDGMGY
VARAGVLG..WLQRA..NV..L.A....HM.KDM..G.Y..TPEE.A.AAKKYNM.VEDY.PY.DDGM.Y
RetrocopyVARAGVLGI*WLQRATQNVVSLSAWPSFHMIKDMPLGFYSKTPEEWATAAKKYNMCVEDYQPYLDDGMEY
ParentalGDYPKLPDRSQHERDPWYSWDQPGLRLNWGEPMHWHLDMYNRNRVDTS-PTPVSWHVMCMQLFGFLAFMI
G.Y.K..D.SQ.ERD.W..WD...LRLNWGE..HWHLD.Y.RN.VD....TPVSW..M...LF.FL.FM.
RetrocopyGNYSKFFDHSQ*ERDLWFDWDHQDLRLNWGELIHWHLDKYIRNHVDMA>STPVSWNIMFNNLFSFLTFMN
ParentalFMCWVGDVYPVYQPVGPKQYPYNNLYLERGGDP-SKEPERVVHYEI
FM..V...Y..YQPVGPKQYP.NNLYL....DP..KEPE.V.HYEI
RetrocopyFMFYVVENYSTYQPVGPKQYPFNNLYLGQDSDP<TKEPELVFHYEI

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 18 .51 RPM
bodymap2_adrenal 0 .00 RPM 40 .69 RPM
bodymap2_brain 0 .00 RPM 47 .07 RPM
bodymap2_breast 0 .08 RPM 26 .34 RPM
bodymap2_colon 0 .02 RPM 40 .18 RPM
bodymap2_heart 0 .02 RPM 35 .11 RPM
bodymap2_kidney 0 .00 RPM 43 .22 RPM
bodymap2_liver 0 .00 RPM 29 .28 RPM
bodymap2_lung 0 .00 RPM 23 .84 RPM
bodymap2_lymph_node 0 .05 RPM 25 .89 RPM
bodymap2_ovary 0 .02 RPM 27 .08 RPM
bodymap2_prostate 0 .03 RPM 36 .13 RPM
bodymap2_skeletal_muscle 0 .00 RPM 11 .33 RPM
bodymap2_testis 0 .00 RPM 25 .56 RPM
bodymap2_thyroid 0 .00 RPM 29 .83 RPM
bodymap2_white_blood_cells 0 .10 RPM 22 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_770 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_770 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_770 retrocopy 5' end.

Lab - click to see more details

retro_hsap_770 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_770 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_539
Gorilla gorilla retro_ggor_639
Pongo abelii retro_pabe_756
Macaca mulatta retro_mmul_1098
Callithrix jacchus retro_cjac_870
Parental genes homology:
Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066513 retrocopies
retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus ENSBTAG000000000911 retrocopy
retro_btau_1844,
Canis familiaris ENSCAFG000000096982 retrocopies
retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus ENSCJAG000000379061 retrocopy
retro_cjac_870,
Dasypus novemcinctus ENSDNOG000000036611 retrocopy
retro_dnov_65,
Felis catus ENSFCAG000000064532 retrocopies
retro_fcat_501, retro_fcat_856,
Homo sapiens ENSG00000166136 3 retrocopies
retro_hsap_1363, retro_hsap_1772, retro_hsap_770 ,
Gorilla gorilla ENSGGOG000000272393 retrocopies
retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus ENSMICG000000013411 retrocopy
retro_mmur_859,
Myotis lucifugus ENSMLUG000000150941 retrocopy
retro_mluc_1830,
Macaca mulatta ENSMMUG000000066365 retrocopies
retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica ENSMODG000000193561 retrocopy
retro_mdom_1543,
Mustela putorius furoENSMPUG000000169591 retrocopy
retro_mputfur_1259,
Mus musculus ENSMUSG000000252042 retrocopies
retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys ENSNLEG000000147743 retrocopies
retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii ENSOGAG000000307113 retrocopies
retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii ENSPPYG000000025703 retrocopies
retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes ENSPTRG000000028513 retrocopies
retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa ENSSSCG000000061662 retrocopies
retro_sscr_1092, retro_sscr_444,
Tupaia belangeri ENSTBEG000000002098 retrocopies
retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,

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 = 0.6 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 .04 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 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .60 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 .11 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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