RetrogeneDB ID:

retro_hsap_4825

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:47372003..47372882(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235636
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NUS1
Ensembl ID:ENSG00000153989
Aliases:NUS1, C6orf68, MGC:7199, NgBR, TANGO14
Description:nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]


Retrocopy-Parental alignment summary:






>retro_hsap_4825
ATGACGGGGCTGTACGAGCTGGTGTGGCGGGTGCTGCACGCGCTGCTCTGTCTGCACCGCACGCTCACCTCCTGGCTCCG
CGTTCGGTTCGGCACCTGGAACTGGATCTGGCGGCGCTGCTGCCGAGCCGCCTCTGCCGCGGTCCTAGCGCCGCTCGGCT
TCACGCTCCGCAAGCCCCCGGCAGTCGGCAGGAACCGCCGTCACCACCGGCACCCGCGCGGGGGGTCGTGCCTGGCAGCC
GCACACCACCGGATGCGCTGGCGCGCGGACGGTCGTTCCTTGGAGAAGCTGCCTGTGCATATGGGCCTGGTGATCACCGA
GGTGGAGCAGGAACCCAGCTTCTCGGACATCGCGAGCCTCGTGGTGTGGTGTATGGCCGTGGGCATCTCCTACATTAGCG
TCTACGACCACCAAGGTATTTTCAAAAGAAATAATTCCAGATTGATGGATGAAATTTTAAAACAACAGCAAGAACTTCTG
GGCCTAGATTGTTCAAAATACTCACCAGAATTTGCAAATAGTAATGACAAAGACGATCAAGTTTTAAATTGCCATTTGGC
AGTGAAGGTGCTGTCTCCGGAAGATGGAAAAGCAGATATTGTAAGAGCTGCTCAGGACTTTTGCCAGTTAGTGGCCCAGA
AGCAAAAGAGACCCACAGATTTGGATGTAGATACGTTAGGCAGTTTACTTAGTTCAAATGGTTGTCCTGATCCTGATTTA
GTATTGAAGTTCGGTCCTGTGGACAGCACATTAGGCTTTCTTCCCTGGCACATCAGATTGACTGAGATTGTCTCTTTGCC
TTCCCACCTAAACATCAGTTATGAGGACTTTTTCTCTGCCCTTCGTCAATATGCAGCCTGTGAACAGCGTCTGGGAAAG

ORF - retro_hsap_4825 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.66 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTGLYELVWRVLHALLCLHRTLTSWLRVRFGTWNWIWRRCCRAASAAVLAPLGFTLRKPPAVGRNRRHHR
MTGLYELVWRVLHALLCLHRTLTSWLRVRFGTWNWIWRRCCRAASAAVLAPLGFTLRKPPAVGRNRRHHR
RetrocopyMTGLYELVWRVLHALLCLHRTLTSWLRVRFGTWNWIWRRCCRAASAAVLAPLGFTLRKPPAVGRNRRHHR
ParentalHPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPSFSDIASLVVWCMAVGISYISVYDHQGI
HPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPSFSDIASLVVWCMAVGISYISVYDHQGI
RetrocopyHPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPSFSDIASLVVWCMAVGISYISVYDHQGI
ParentalFKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCHLAVKVLSPEDGKADIVRAAQDFCQL
FKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCHLAVKVLSPEDGKADIVRAAQDFCQL
RetrocopyFKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVLNCHLAVKVLSPEDGKADIVRAAQDFCQL
ParentalVAQKQKRPTDLDVDTLASLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIVSLPSHLNISYEDFFSA
VAQKQKRPTDLDVDTL.SLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIVSLPSHLNISYEDFFSA
RetrocopyVAQKQKRPTDLDVDTLGSLLSSNGCPDPDLVLKFGPVDSTLGFLPWHIRLTEIVSLPSHLNISYEDFFSA
ParentalLRQYAACEQRLGK
LRQYAACEQRLGK
RetrocopyLRQYAACEQRLGK

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 1 .31 RPM 33 .71 RPM
bodymap2_adrenal 0 .72 RPM 42 .09 RPM
bodymap2_brain 0 .54 RPM 26 .89 RPM
bodymap2_breast 0 .33 RPM 30 .64 RPM
bodymap2_colon 1 .30 RPM 47 .66 RPM
bodymap2_heart 0 .98 RPM 21 .21 RPM
bodymap2_kidney 1 .37 RPM 58 .59 RPM
bodymap2_liver 1 .46 RPM 49 .85 RPM
bodymap2_lung 1 .49 RPM 38 .40 RPM
bodymap2_lymph_node 1 .70 RPM 46 .52 RPM
bodymap2_ovary 0 .79 RPM 45 .07 RPM
bodymap2_prostate 1 .21 RPM 40 .53 RPM
bodymap2_skeletal_muscle 0 .31 RPM 11 .55 RPM
bodymap2_testis 1 .06 RPM 38 .72 RPM
bodymap2_thyroid 0 .81 RPM 42 .11 RPM
bodymap2_white_blood_cells 2 .44 RPM 57 .29 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_4825 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CJZ POLR2A X:47373779..47374653
ENCFF002CJZ POLR2A X:47373013..47373535
ENCFF002CSY POLR2A X:47372792..47372994

EST - click to see more details

No EST(s) were mapped for retro_hsap_4825 retrocopy.

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_1999261622 libraries183 libraries22 libraries2 libraries0 libraries
TSS #2 TSS_1999271670 libraries147 libraries10 libraries2 libraries0 libraries

The graphical summary, for retro_hsap_4825 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_4825 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4825 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000017801 retrocopy
retro_dnov_1639,
Erinaceus europaeus ENSEEUG000000089481 retrocopy
retro_eeur_443,
Homo sapiens ENSG00000153989 4 retrocopies
retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825 ,
Gorilla gorilla ENSGGOG000000223214 retrocopies
retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus ENSMICG000000078311 retrocopy
retro_mmur_423,
Nomascus leucogenys ENSNLEG000000134571 retrocopy
retro_nleu_2411,
Oryctolagus cuniculus ENSOCUG000000115531 retrocopy
retro_ocun_1713,
Pongo abelii ENSPPYG000000258861 retrocopy
retro_pabe_81,
Pan troglodytes ENSPTRG000000185471 retrocopy
retro_ptro_808,
Tarsius syrichta ENSTSYG000000032121 retrocopy
retro_tsyr_633,
Tursiops truncatus ENSTTRG000000073522 retrocopies
retro_ttru_358, retro_ttru_684,

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 = 2.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .20 RPM
CEU_NA11843 0 .54 RPM
CEU_NA11930 1 .24 RPM
CEU_NA12004 0 .99 RPM
CEU_NA12400 0 .67 RPM
CEU_NA12751 1 .14 RPM
CEU_NA12760 1 .12 RPM
CEU_NA12827 1 .08 RPM
CEU_NA12872 0 .65 RPM
CEU_NA12873 1 .15 RPM
FIN_HG00183 2 .03 RPM
FIN_HG00277 1 .11 RPM
FIN_HG00315 0 .75 RPM
FIN_HG00321 0 .79 RPM
FIN_HG00328 0 .66 RPM
FIN_HG00338 0 .62 RPM
FIN_HG00349 1 .00 RPM
FIN_HG00375 1 .17 RPM
FIN_HG00377 0 .78 RPM
FIN_HG00378 1 .76 RPM
GBR_HG00099 0 .99 RPM
GBR_HG00111 0 .75 RPM
GBR_HG00114 0 .84 RPM
GBR_HG00119 1 .13 RPM
GBR_HG00131 1 .78 RPM
GBR_HG00133 0 .99 RPM
GBR_HG00134 0 .87 RPM
GBR_HG00137 1 .02 RPM
GBR_HG00142 1 .11 RPM
GBR_HG00143 0 .64 RPM
TSI_NA20512 0 .42 RPM
TSI_NA20513 0 .97 RPM
TSI_NA20518 1 .36 RPM
TSI_NA20532 0 .82 RPM
TSI_NA20538 1 .57 RPM
TSI_NA20756 0 .93 RPM
TSI_NA20765 1 .02 RPM
TSI_NA20771 1 .50 RPM
TSI_NA20786 0 .76 RPM
TSI_NA20798 1 .09 RPM
YRI_NA18870 1 .46 RPM
YRI_NA18907 1 .28 RPM
YRI_NA18916 0 .61 RPM
YRI_NA19093 1 .33 RPM
YRI_NA19099 0 .77 RPM
YRI_NA19114 1 .18 RPM
YRI_NA19118 1 .08 RPM
YRI_NA19213 1 .00 RPM
YRI_NA19214 0 .79 RPM
YRI_NA19223 0 .92 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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