RetrogeneDB ID:

retro_hsap_477

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:174818853..174819306(-)
Located in intron of:ENSG00000152061
Retrocopy
information
Ensembl ID:ENSG00000231378
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFAF4
Ensembl ID:ENSG00000123545
Aliases:NDUFAF4, C6orf66, HRPAP20, My013, bA22L21.1
Description:NADH dehydrogenase (ubiquinone) complex I, assembly factor 4 [Source:HGNC Symbol;Acc:21034]


Retrocopy-Parental alignment summary:






>retro_hsap_477
ATGGGGGCTGCAGTGACTCGCAGGATCAGGAATTTCAACCTAGAGAACTGAGAGGAATGGGAAATCAACAAGATGAAGCC
CCCTCCCAATCCCAGACACCCCTCTACCAACAGCCTCCTGCAAGAGCAGATTAGTTTCTATCCAGAAATTAAGGGAGAGA
TTGCTCATAAAGATGACAAGCTGCTGTCATTTCTAAAAGATGTGTATGTTGATTCCAAAGATCCTGTGTCTTCCATGCAG
GTAAAAGCTGCTGAAAGATGTCAAGAGCTGAAAGAATTCAGATTGCCTTTTGGCCATCACTTTAATATGATAAATATTAA
GATCATTCCCAAAGGCAAAATTTCCATTGTAGAAGCATTGACACTTCTCAATAATCATAAACTTTATCCAGAAACATGAA
CTGCTGAGAAAATAGCCCAAGAATACCATTTAGAACAGAAAGATGCGAATTCA

ORF - retro_hsap_477 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.12 %
Parental protein coverage: 86.29 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGALVIRGIRNFNLENRAEREISKMKPSVAPRHPSTNSLLREQISLYPEVKGEIARKDEKLLSFLKDVYV
MGA.V.R.IRNFNLEN..E.EI.KMKP...PRHPSTNSLL.EQIS.YPE.KGEIA.KD.KLLSFLKDVYV
RetrocopyMGAAVTRRIRNFNLEN*EEWEINKMKPPPNPRHPSTNSLLQEQISFYPEIKGEIAHKDDKLLSFLKDVYV
ParentalDSKDPVSSLQVKAAETCQEPKEFRLPKDHHFDMINIKSIPKGKISIVEALTLLNNHKLFPETWTAEKIMQ
DSKDPVSS.QVKAAE.CQE.KEFRLP..HHF.MINIK.IPKGKISIVEALTLLNNHKL.PET.TAEKI.Q
RetrocopyDSKDPVSSMQVKAAERCQELKEFRLPFGHHFNMINIKIIPKGKISIVEALTLLNNHKLYPET*TAEKIAQ
ParentalEYQLEQKDVNS
EY.LEQKD.NS
RetrocopyEYHLEQKDANS

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 11 .07 RPM
bodymap2_adrenal 0 .12 RPM 18 .42 RPM
bodymap2_brain 0 .00 RPM 53 .26 RPM
bodymap2_breast 0 .02 RPM 20 .47 RPM
bodymap2_colon 0 .00 RPM 25 .39 RPM
bodymap2_heart 0 .09 RPM 45 .54 RPM
bodymap2_kidney 0 .06 RPM 45 .99 RPM
bodymap2_liver 0 .00 RPM 17 .70 RPM
bodymap2_lung 0 .00 RPM 10 .69 RPM
bodymap2_lymph_node 0 .00 RPM 26 .02 RPM
bodymap2_ovary 0 .04 RPM 27 .32 RPM
bodymap2_prostate 0 .00 RPM 31 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 24 .64 RPM
bodymap2_testis 0 .00 RPM 29 .01 RPM
bodymap2_thyroid 0 .09 RPM 42 .39 RPM
bodymap2_white_blood_cells 0 .00 RPM 8 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_477 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_477 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_477 retrocopy 5' end.

Lab - click to see more details

Experiment type: PCR amplification
Forward primer: AGGTTTCCTGCACTGGTGTT (20 nt long)
Reverse primer: CCATTCCTCTCAGTTCTCTAGGTT (24 nt long)
Anneling temperature: 55 °C
(Expected) product size: 122
Electrophoresis gel image:
Additional comment: Black arrows indicate PCR products of retrogenes undergoing deletions in various human populations (A-J). Lane 1 –GeneRuler Low Range DNA Ladder (Thermo Scientific); 2 –Heart; 3 –Brain; 4 –Placenta; 5 –Lung; 6 –Liver; 7 –Skeletal Muscle; 8 –Kidney; 9 –Pancreas; 10 –Spleen; 11 –Thymus; 12 –Prostate; 13 –Testis; 14 –Ovary, 15 –Small intestine 16 –Colon; 17 –Leukocyte; NTC—No template control (water instead of cDNA).

Retrocopy orthology:
Retrocopy retro_hsap_477 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_358
Pongo abelii retro_pabe_257
Parental genes homology:
Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000031741 retrocopy
retro_btau_1763,
Choloepus hoffmanni ENSCHOG000000051452 retrocopies
retro_chof_2271, retro_chof_891,
Callithrix jacchus ENSCJAG000000012352 retrocopies
retro_cjac_1613, retro_cjac_1700,
Cavia porcellus ENSCPOG000000076181 retrocopy
retro_cpor_425,
Homo sapiens ENSG00000123545 4 retrocopies
retro_hsap_1494, retro_hsap_2774, retro_hsap_3761, retro_hsap_477 ,
Gorilla gorilla ENSGGOG000000120704 retrocopies
retro_ggor_1147, retro_ggor_1931, retro_ggor_2529, retro_ggor_451,
Microcebus murinus ENSMICG000000157341 retrocopy
retro_mmur_1624,
Macaca mulatta ENSMMUG000000188434 retrocopies
retro_mmul_1717, retro_mmul_2138, retro_mmul_578, retro_mmul_734,
Mus musculus ENSMUSG000000282613 retrocopies
retro_mmus_1153, retro_mmus_1290, retro_mmus_3668,
Nomascus leucogenys ENSNLEG000000135684 retrocopies
retro_nleu_171, retro_nleu_1716, retro_nleu_678, retro_nleu_890,
Oryctolagus cuniculus ENSOCUG000000021521 retrocopy
retro_ocun_1162,
Pongo abelii ENSPPYG000000168574 retrocopies
retro_pabe_1244, retro_pabe_2241, retro_pabe_257, retro_pabe_3160,
Pan troglodytes ENSPTRG000000184354 retrocopies
retro_ptro_1013, retro_ptro_1877, retro_ptro_2552, retro_ptro_358,
Rattus norvegicus ENSRNOG000000075063 retrocopies
retro_rnor_1617, retro_rnor_2973, retro_rnor_675,
Tursiops truncatus ENSTTRG000000109111 retrocopy
retro_ttru_628,

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 = 0.2 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .07 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 .10 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .00 RPM

Indel association:

The presence of retro_hsap_477 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_477 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 1:174802989..174819000 100 100 100 100 100 100 100 100 100 100 100 100 98.97 99.5

Indel #1, located at the genomic coordinates 1:174802989..174819000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 98.97 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 99.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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