RetrogeneDB ID:

retro_hsap_2984

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:139481857..139483092(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248795
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NOB1
Ensembl ID:ENSG00000141101
Aliases:NOB1, ART-4, MST158, NOB1P, PSMD8BP1
Description:NIN1/RPN12 binding protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29540]


Retrocopy-Parental alignment summary:






>retro_hsap_2984
GTGGCTCCAGTGGAGCAAGTTGTGGCGGATGCTGGGGCTTTCCTTCGGGATGCGGCTCTGCAGGACATCGGGAAGAACAT
TTACATCATCCGGGAGGTGGTCACTGAGTTTCGGGACAAGGCCACATGCAGGCGGCTCGCTGTCCTGCCCTATGAGCTGC
GGTTCAAGGAGCCCTTACCAGAATACGTGCAGCTGGTGACTGAGTTTTCAAAGAAAACAGGAGACTACCCCAGCCTCTCT
GCCACGGACATCCAAGTGCTTGCGCTCACATACCAGTTGGAAGCAGAGTTTGTTGGGGTGTCTCACCTAAAACAAGAACC
ACAGAAGGTTAAACTGAGCTCATCGATTCAGCACCCAGAAACACCTCTGCACATTTCTGGTTTCCATCTGCCCTCCAAGC
CTAAACCCCCACAAGAAACAGAAAAAGGACACCCAGCTTGTGAGCCTGAGAACCTGGAATTTAGTTCCTTCATGTTCCGG
AGAAACCCTCTGCCCAACATCGATCATGAACTGCAGGAGCCGCTGATTGACAGAGGTGAGGACGTTCCAAGAGAGGAGGA
GGAGGAGGAAGAAAACGGGTTTGAAGACAGAAAAGATGACAGCGATGACGACGGGGGTGGCTGGATAACCCCCAGTAACA
TCAAGCAGATCCAGCAGGAGCTGGAGCAGTGCGACGTCCCCGAGGACGTGCGGGTTGGCTGCGTGACCACAGACTTCCCC
AGGCAGAATGTTCTGCTGCAGATGGGGCTGCACGTGCTGGCGGTGAACTGCATGCTGATTCGTGAGGCCCAGAGCTACGT
CTGGGCTGCCACGGCTGTTTCAAGACAACGTCTGACATGAGCCGAGTGTTCTGTTCACACTGTGGGAACAAGACCCTGAA
GAAAGTGTCCGTGACCATCAGTGACGACGGCACCCTGCACATGCACTTCTCCCGCAACCCCAAGGTGCTGAACGCCCGCG
GCCTCCGGTACTCGCTTCCCACTCCCAAAGGGGGCACATACGCCATCAACCCCCATCTCACCGAGGATCAGCGCTTCCCT
CAACCGCGACTCTCCCGAAAGGCCAGGCAGAAAACCAACGTGTTCGCCCCTGACTACATCGCCGGGATGTCGCCCTTTGT
CGAGAATGACATCTCCAGCCGCTCAGCTACCCTACAGGTCCGGGACAGCACCTTGGGAGCTGGGCGGAGACGCTTAAATC
CCAACGCTTCCAGAAAGAAGTTTGTGAAGAAAAGG

ORF - retro_hsap_2984 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.46 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAPVEHVVADAGAFLRHAALQDIGKNIYTIREVVTEIRDKATRRRLAVLPYELRFKEPLPEYVRLVTEFS
.APVE.VVADAGAFLR.AALQDIGKNIY.IREVVTE.RDKAT.RRLAVLPYELRFKEPLPEYV.LVTEFS
RetrocopyVAPVEQVVADAGAFLRDAALQDIGKNIYIIREVVTEFRDKATCRRLAVLPYELRFKEPLPEYVQLVTEFS
ParentalKKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVKVSSSIQHPETPLHISGFHLPYKPKPPQET
KKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVK.SSSIQHPETPLHISGFHLP.KPKPPQET
RetrocopyKKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVKLSSSIQHPETPLHISGFHLPSKPKPPQET
ParentalEKGHSACEPENLEFSSFMFWRNPLPNIDHELQELLIDRGEDVPSEEEEEEENGFEDRKDDSDDDGGGWIT
EKGH.ACEPENLEFSSFMF.RNPLPNIDHELQE.LIDRGEDVP.EEEEEEENGFEDRKDDSDDDGGGWIT
RetrocopyEKGHPACEPENLEFSSFMFRRNPLPNIDHELQEPLIDRGEDVPREEEEEEENGFEDRKDDSDDDGGGWIT
ParentalPSNIKQIQQELEQCDVPEDVRVGCLTTDFAMQNVLLQMGLHVLAVNGMLIREARSYI-LRCHGCFKTTSD
PSNIKQIQQELEQCDVPEDVRVGC.TTDF..QNVLLQMGLHVLAVN.MLIREA.SY..L.CHGCFKTTSD
RetrocopyPSNIKQIQQELEQCDVPEDVRVGCVTTDFPRQNVLLQMGLHVLAVNCMLIREAQSYV<LGCHGCFKTTSD
ParentalMSRVFCSHCGNKTLKKVSVTVSDDGTLHMHFSRNPKVLNPRGLRYSLPTPKGGKYAINPHLTEDQRFPQL
MSRVFCSHCGNKTLKKVSVT.SDDGTLHMHFSRNPKVLN.RGLRYSLPTPKGG.YAINPHLTEDQRFPQ.
RetrocopyMSRVFCSHCGNKTLKKVSVTISDDGTLHMHFSRNPKVLNARGLRYSLPTPKGGTYAINPHLTEDQRFPQP
ParentalRLSQKARQKTNVFAPDYIAGVSPFVENDISSRSATLQVRDSTLGAGRRRLNPNASRKKFVKKR
RLS.KARQKTNVFAPDYIAG.SPFVENDISSRSATLQVRDSTLGAGRRRLNPNASRKKFVKKR
RetrocopyRLSRKARQKTNVFAPDYIAGMSPFVENDISSRSATLQVRDSTLGAGRRRLNPNASRKKFVKKR

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 .10 RPM 27 .05 RPM
bodymap2_adrenal 0 .04 RPM 27 .98 RPM
bodymap2_brain 0 .00 RPM 8 .72 RPM
bodymap2_breast 0 .02 RPM 18 .54 RPM
bodymap2_colon 0 .02 RPM 24 .32 RPM
bodymap2_heart 0 .00 RPM 6 .22 RPM
bodymap2_kidney 0 .00 RPM 17 .00 RPM
bodymap2_liver 0 .00 RPM 12 .59 RPM
bodymap2_lung 0 .00 RPM 17 .26 RPM
bodymap2_lymph_node 0 .00 RPM 25 .88 RPM
bodymap2_ovary 0 .00 RPM 36 .11 RPM
bodymap2_prostate 0 .02 RPM 28 .91 RPM
bodymap2_skeletal_muscle 0 .02 RPM 21 .92 RPM
bodymap2_testis 0 .21 RPM 19 .61 RPM
bodymap2_thyroid 0 .02 RPM 33 .50 RPM
bodymap2_white_blood_cells 0 .00 RPM 28 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2984 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2984 retrocopy
EST ID Start End Identity Match Mis-match Score
DB049656 139481829 139482398 99.3 565 4 561

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_1399001479 libraries315 libraries35 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_2984 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_2984 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2984 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2019
Gorilla gorilla retro_ggor_2067
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000143841 retrocopy
retro_eeur_450,
Homo sapiens ENSG00000141101 1 retrocopy
retro_hsap_2984 ,
Gorilla gorilla ENSGGOG000000254561 retrocopy
retro_ggor_2067,
Pan troglodytes ENSPTRG000000082851 retrocopy
retro_ptro_2019,

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 = 0.38 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 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 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .38 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .02 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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