RetrogeneDB ID:

retro_hsap_4698

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:70911867..70912029(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230934
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA4L2
Ensembl ID:ENSG00000185633
Aliases:NDUFA4L2, NUOMS
Description:NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 [Source:HGNC Symbol;Acc:29836]


Retrocopy-Parental alignment summary:






>retro_hsap_4698
GCAGGGCTGCATGTCTTGCATCTGACACTGTTTAACCCAAAAGTTAGTTGGGACAGAAAGAATACCTCAGAATCCTGGAA
TAAACGGGGTCCCGATGATCAATACGAGTTCTACTCAGCGAATGCAGATTACAGCAAACGGAAGAAAGAATGTCCAGACT
TC

ORF - retro_hsap_4698 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.85 %
Parental protein coverage: 62.07 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAALYLLRLALRSPDVCWDRKNNPEPWNRLSPNDQYKFLAVSTDYKKLKKDRPDF
A.L..L.L.L..P.V.WDRKN..E.WN...P.DQY.F.....DY.K.KK..PDF
RetrocopyAGLHVLHLTLFNPKVSWDRKNTSESWNKRGPDDQYEFYSANADYSKRKKECPDF

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 24 .23 RPM
bodymap2_adrenal 0 .00 RPM 14 .14 RPM
bodymap2_brain 0 .00 RPM 6 .16 RPM
bodymap2_breast 0 .00 RPM 13 .60 RPM
bodymap2_colon 0 .00 RPM 15 .12 RPM
bodymap2_heart 0 .00 RPM 11 .46 RPM
bodymap2_kidney 0 .00 RPM 2 .38 RPM
bodymap2_liver 0 .00 RPM 0 .44 RPM
bodymap2_lung 0 .00 RPM 21 .55 RPM
bodymap2_lymph_node 0 .00 RPM 11 .62 RPM
bodymap2_ovary 0 .00 RPM 3 .60 RPM
bodymap2_prostate 0 .00 RPM 6 .89 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .53 RPM
bodymap2_testis 0 .00 RPM 6 .75 RPM
bodymap2_thyroid 0 .00 RPM 6 .55 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4698 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4698 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4698 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4698 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4698 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000044661 retrocopy
retro_etel_52,
Homo sapiens ENSG00000185633 2 retrocopies
retro_hsap_4698 , retro_hsap_4857,
Homo sapiens ENSG0000018904318 retrocopies
retro_hsap_1459, retro_hsap_200, retro_hsap_2374, retro_hsap_2386, retro_hsap_259, retro_hsap_2685, retro_hsap_2726, retro_hsap_285, retro_hsap_3241, retro_hsap_4067, retro_hsap_4188, retro_hsap_4292, retro_hsap_4699, retro_hsap_4700, retro_hsap_4750, retro_hsap_4856, retro_hsap_650, retro_hsap_877,
Loxodonta africana ENSLAFG000000219501 retrocopy
retro_lafr_21,
Macropus eugenii ENSMEUG000000143583 retrocopies
retro_meug_1159, retro_meug_1559, retro_meug_467,
Nomascus leucogenys ENSNLEG0000001737110 retrocopies
retro_nleu_1015, retro_nleu_1048, retro_nleu_1851, retro_nleu_1917, retro_nleu_2588, retro_nleu_2952, retro_nleu_363, retro_nleu_732, retro_nleu_862, retro_nleu_956,
Ictidomys tridecemlineatus ENSSTOG000000204761 retrocopy
retro_itri_23,
Tupaia belangeri ENSTBEG000000157315 retrocopies
retro_tbel_3586, retro_tbel_4134, retro_tbel_4193, retro_tbel_822, retro_tbel_865,

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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