RetrogeneDB ID:

retro_hsap_2585

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:36293313..36294452(-)
Located in intron of:ENSG00000100320
Retrocopy
information
Ensembl ID:ENSG00000237406
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA9
Ensembl ID:ENSG00000139180
Aliases:None
Description:NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa [Source:HGNC Symbol;Acc:7693]


Retrocopy-Parental alignment summary:






>retro_hsap_2585
ATGGCGGCCGCTGCACAATCCCGGGTTGTCTGGGCCCTGCCAATGTCACATTCTGCCATTACTGCAATAGCCACATCCGT
GTGTCACAGCCCACTCCATTGCCAGCTTCATCATGCCCTCATACCTCATGGGAAAGGTGAATGTTCCTCAAGTCAGTGGG
ATTGTGGCCACTGGGTTTGGAGCAACAGGATTCCTGGGCCGATGTGTTGTCAACCACCTTGGACGCGTGGGGTCACAGGT
GATCATACCCTATCGGTGTGATACATGTGACATCATGCACCTTCGTCCCATGGGAGACCTGGGCTAGCTTCTGTTTCTGG
AATGGGACGCGAGAGATAAAGATTCTATCTGACGAGTAGTGGAACACAGCAATGTGGTCATAAATCTTGTTGGACGAGAC
TGGGAAACCAAAAACTTTGATTTTGAGGATGTTTTTGTGAAGATTCCCCAAGCAATTGCTCAGGTGTCCAAGGAAGCTGA
AGTTGGAAAATTCATTCATGTTGCACATCTGAATGTGAATATTAAAAGCTCTTCTAGATATTTGAGAAAGAAGGCTGTTG
GAGAGAAAGCAGTGAGAGACACATTTCCAGAAGCCATTATCGTAAAGCTGTTGGACATCTTTGGAAGAGAGGATAGATTC
CTTAATTATTTTGCAAATATGTGTTGGTTTGGTGCTATACCCCTTGTTTCCTTGGGCTGGAAGGCAGTTAAACAACCAGT
ATACGTCGTAGATGTATCCAAAGGAATTGTTAATGCAGTTAAGGATCCTGATGCCAATGGGAAAACCTTTGCTTTCGTTG
GGCCAAATCGATATCTCCTCTTTGACCTGGTGAAGTACATCTTTGCTGTGGCTCACAGCAAAGGGGTACTTCCTCCCGTA
CCCCTTGCCACCTTTTGCCTATCAGTGGGTAGCAAGAGACTTTGAAATAAGCCCATTTGAGTCCTGGACAACAAGGGATA
AAGTGGAGCGTATTCACATCACAGACATGACCTTGTCTCACCTGCCCAGCTTAGAAGACCTTGGTATTCAGGCAACACCA
CTGGAACTCAAGGCCATTGAGGTGCTGCGGCTTCATCACACTTACTGCTGGCTGTCTGCTGAAATTGAGGATGTGAAGCT
GGCCAAGACCGTCAACATT

ORF - retro_hsap_2585 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.73 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAAAAQSRVVRVLSMSRSAITAIATSVCHGPPCRQLHHALMPHGKGGRSS-VSGIVATVFGATGFLGRYV
MAAAAQSRVV..L.MS.SAITAIATSVCH.P...QLHHAL.PHGKG..SS.VSGIVAT.FGATGFLGR.V
RetrocopyMAAAAQSRVVWALPMSHSAITAIATSVCHSPLHCQLHHALIPHGKGECSS>VSGIVATGFGATGFLGRCV
ParentalVNHLGRMGSQVIIPYRCDKYDIMHLRPMGDLGQLLFLEWDARDKDSIRRVVQHSNVVINLIGRDWETKNF
VNHLGR.GSQVIIPYRCD..DIMHLRPMGDLG.LLFLEWDARDKDSI.RVV.HSNVVINL.GRDWETKNF
RetrocopyVNHLGRVGSQVIIPYRCDTCDIMHLRPMGDLG*LLFLEWDARDKDSI*RVVEHSNVVINLVGRDWETKNF
ParentalDFEDVFVKIPQAIAQLSKEAGVEKFIHVSHLNANIKSSSRYLRNKAVGEKVVRDAFPEAIIVKPSDIFGR
DFEDVFVKIPQAIAQ.SKEA.V.KFIHV.HLN.NIKSSSRYLR.KAVGEK.VRD.FPEAIIVK..DIFGR
RetrocopyDFEDVFVKIPQAIAQVSKEAEVGKFIHVAHLNVNIKSSSRYLRKKAVGEKAVRDTFPEAIIVKLLDIFGR
ParentalEDRFLNSFASMHRFGPIPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKY
EDRFLN.FA.M..FG.IPL.SLGWK.VKQPVYVVDVSKGIVNAVKDPDANGK.FAFVGP.RYLLF.LVKY
RetrocopyEDRFLNYFANMCWFGAIPLVSLGWKAVKQPVYVVDVSKGIVNAVKDPDANGKTFAFVGPNRYLLFDLVKY
ParentalIFAVAHR--LFLPFP-LPLFAYRWVARVFEISPFEPWITRDKVERMHITDMKLPHLPGLEDLGIQATPLE
IFAVAH......P.P.LP.FAY.WVAR.FEISPFE.W.TRDKVER.HITDM.L.HLP.LEDLGIQATPLE
RetrocopyIFAVAHSKGVLPPVP>LPPFAYQWVARDFEISPFESWTTRDKVERIHITDMTLSHLPSLEDLGIQATPLE
ParentalLKAIEVLRRHRTYRWLSAEIEDVKPAKTVNI
LKAIEVLR.H.TY.WLSAEIEDVK.AKTVNI
RetrocopyLKAIEVLRLHHTYCWLSAEIEDVKLAKTVNI

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 .14 RPM 18 .45 RPM
bodymap2_adrenal 0 .12 RPM 32 .46 RPM
bodymap2_brain 0 .07 RPM 26 .07 RPM
bodymap2_breast 0 .14 RPM 27 .26 RPM
bodymap2_colon 0 .02 RPM 19 .32 RPM
bodymap2_heart 0 .06 RPM 62 .21 RPM
bodymap2_kidney 0 .04 RPM 47 .05 RPM
bodymap2_liver 0 .06 RPM 24 .91 RPM
bodymap2_lung 0 .00 RPM 14 .59 RPM
bodymap2_lymph_node 0 .00 RPM 17 .10 RPM
bodymap2_ovary 0 .13 RPM 20 .95 RPM
bodymap2_prostate 0 .09 RPM 24 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 33 .88 RPM
bodymap2_testis 0 .00 RPM 17 .85 RPM
bodymap2_thyroid 0 .02 RPM 30 .39 RPM
bodymap2_white_blood_cells 0 .00 RPM 24 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2585 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2585 retrocopy
EST ID Start End Identity Match Mis-match Score
BE090973 36293309 36293800 99.2 487 4 483

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1082661708 libraries95 libraries21 libraries0 libraries5 libraries

The graphical summary, for retro_hsap_2585 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2585 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2585 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1511
Gorilla gorilla retro_ggor_1618
Pongo abelii retro_pabe_1905
Macaca mulatta retro_mmul_648
Parental genes homology:
Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000095881 retrocopy
retro_acar_16,
Danio rerio ENSDARG000000707231 retrocopy
retro_drer_1,
Homo sapiens ENSG00000139180 1 retrocopy
retro_hsap_2585 ,
Gorilla gorilla ENSGGOG000000060761 retrocopy
retro_ggor_1618,
Macaca mulatta ENSMMUG000000208131 retrocopy
retro_mmul_648,
Monodelphis domestica ENSMODG000000182831 retrocopy
retro_mdom_209,
Nomascus leucogenys ENSNLEG000000032521 retrocopy
retro_nleu_1520,
Otolemur garnettii ENSOGAG000000052251 retrocopy
retro_ogar_2244,
Pongo abelii ENSPPYG000000041711 retrocopy
retro_pabe_1905,
Pan troglodytes ENSPTRG000000045571 retrocopy
retro_ptro_1511,
Ictidomys tridecemlineatus ENSSTOG000000065041 retrocopy
retro_itri_543,

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 = 0.06 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 .04 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 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .02 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 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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