RetrogeneDB ID:

retro_hsap_2687

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:113604144..113604875(+)
Located in intron of:ENSG00000178075
Retrocopy
information
Ensembl ID:ENSG00000241889
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CTDNEP1
Ensembl ID:ENSG00000175826
Aliases:CTDNEP1, DULLARD, HSA011916, NET56
Description:CTD nuclear envelope phosphatase 1 [Source:HGNC Symbol;Acc:19085]


Retrocopy-Parental alignment summary:






>retro_hsap_2687
ATGGTGCGGACGCAGTGTCTGCTGGGACTGCGCACGTTCGTGGCCTTCGCTGCCAAGCTCTGGAGCTTCTTCATTTACCT
TTTGCGGGGGCAGATCCGCACGGTAATTCAGTACCAAACTGTTCGATATGATATCCTCCCCTTATCTCCTGTGTCCCGGA
ATTGGCTAGCCCAGGTGAGGAGGAAGATCCTGGTGCTGGATCTGGATGAGACACTTATTCACTCCCACCATGATGGGGTC
CTGAGGCCGCAGTCCGGCCTGTTAGGCCTCCTGACTTCATCCTCAAGGTGGTAATAGACAAACATTCTGTCCGGTTTTTT
GTACGTAAGAGGCCCCATGTGGATTTCTTCCTGGAAGTGGTGAGCCAGTGGTACGAGCTGGTGGTGTTTACAGAAAGCAT
GGAGATCTATGGCTTTGCTGTGGCAGGTAAACTGGACAATAGCAGAAGCATCCTTAAGAGGAGATATTACAGACAGCACT
GCACTTTGCAGTTGAGCAGCTACATCAAGGACCTCTCTGTGGTCCACAGTGACCTCTCCAGCATTGTGATCCTGGATAAC
TCCCTAGGGGCTTACAGGAGCCATCCAGACAATGCCATCCCCATCAAATCCTGGTTCAGTGACCCCAGCGACACAGCCCT
TCTCAACCTGCTCCCGATGCTGGATGCCCTCAGGTTCACCGCTGACGTTCATTCTGTGCTGAGCCGAAACCTTCACCAAC
ATCGGCTCTGG

ORF - retro_hsap_2687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.06 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMMRTQCLLGLRTFVAFAAKLWSFFIYLLRRQIRTVIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDE
M.RTQCLLGLRTFVAFAAKLWSFFIYLLR.QIRTVIQYQTVRYDILPLSPVSRN.LAQV.RKILVLDLDE
RetrocopyMVRTQCLLGLRTFVAFAAKLWSFFIYLLRGQIRTVIQYQTVRYDILPLSPVSRNWLAQVRRKILVLDLDE
ParentalTLIHSHHDGVLRP-TVRPGTPPDFILKVVIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYGS
TLIHSHHDGVLRP..VRP..PPDFILKVVIDKH.VRFFV.KRPHVDFFLEVVSQWYELVVFT.SMEIYG.
RetrocopyTLIHSHHDGVLRP<AVRPVRPPDFILKVVIDKHSVRFFVRKRPHVDFFLEVVSQWYELVVFTESMEIYGF
ParentalAVADKLDNSRSILKRRYYRQHCTLELGSYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDP
AVA.KLDNSRSILKRRYYRQHCTL.L.SYIKDLSVVHSDLSSIVILDNS.GAYRSHPDNAIPIKSWFSDP
RetrocopyAVAGKLDNSRSILKRRYYRQHCTLQLSSYIKDLSVVHSDLSSIVILDNSLGAYRSHPDNAIPIKSWFSDP
ParentalSDTALLNLLPMLDALRFTADVRSVLSRNLHQHRLW
SDTALLNLLPMLDALRFTADV.SVLSRNLHQHRLW
RetrocopySDTALLNLLPMLDALRFTADVHSVLSRNLHQHRLW

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 .06 RPM 77 .44 RPM
bodymap2_adrenal 0 .39 RPM 87 .67 RPM
bodymap2_brain 0 .12 RPM 49 .01 RPM
bodymap2_breast 0 .00 RPM 76 .62 RPM
bodymap2_colon 0 .02 RPM 85 .43 RPM
bodymap2_heart 0 .07 RPM 40 .43 RPM
bodymap2_kidney 0 .14 RPM 57 .53 RPM
bodymap2_liver 0 .06 RPM 21 .48 RPM
bodymap2_lung 0 .07 RPM 67 .81 RPM
bodymap2_lymph_node 0 .15 RPM 97 .07 RPM
bodymap2_ovary 0 .08 RPM 85 .34 RPM
bodymap2_prostate 0 .23 RPM 76 .17 RPM
bodymap2_skeletal_muscle 0 .04 RPM 169 .69 RPM
bodymap2_testis 0 .11 RPM 72 .64 RPM
bodymap2_thyroid 0 .40 RPM 83 .86 RPM
bodymap2_white_blood_cells 0 .08 RPM 123 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2687 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2687 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_1276131207 libraries299 libraries304 libraries17 libraries2 libraries
TSS #2 TSS_1276141113 libraries596 libraries107 libraries13 libraries0 libraries

The graphical summary, for retro_hsap_2687 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_2687 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2687 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1814
Gorilla gorilla retro_ggor_1874
Pongo abelii retro_pabe_2294
Parental genes homology:
Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000194431 retrocopy
retro_btau_915,
Dasypus novemcinctus ENSDNOG000000136732 retrocopies
retro_dnov_1802, retro_dnov_2494,
Echinops telfairi ENSETEG000000046541 retrocopy
retro_etel_125,
Homo sapiens ENSG00000175826 2 retrocopies
retro_hsap_2687 , retro_hsap_3188,
Gorilla gorilla ENSGGOG000000137772 retrocopies
retro_ggor_1338, retro_ggor_1874,
Macaca mulatta ENSMMUG000000105471 retrocopy
retro_mmul_2011,
Mus musculus ENSMUSG000000185591 retrocopy
retro_mmus_1023,
Otolemur garnettii ENSOGAG000000043891 retrocopy
retro_ogar_1001,
Pongo abelii ENSPPYG000000079022 retrocopies
retro_pabe_2294, retro_pabe_2645,
Pan troglodytes ENSPTRG000000086682 retrocopies
retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster FBgn00290671 retrocopy
retro_dmel_18,

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 = 0.29 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .23 RPM
CEU_NA11930 0 .29 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .27 RPM
FIN_HG00377 0 .15 RPM
FIN_HG00378 0 .19 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .19 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .20 RPM
GBR_HG00137 0 .22 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .15 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .10 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .12 RPM
YRI_NA19223 0 .10 RPM

Indel association:

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



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