RetrogeneDB ID:

retro_hsap_4050

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:48423605..48424703(-)
Located in intron of:ENSG00000164808
Retrocopy
information
Ensembl ID:ENSG00000253330
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NSFL1C
Ensembl ID:ENSG00000088833
Aliases:NSFL1C, P47, UBX1, UBXD10, UBXN2C, dJ776F14.1
Description:NSFL1 (p97) cofactor (p47) [Source:HGNC Symbol;Acc:15912]


Retrocopy-Parental alignment summary:






>retro_hsap_4050
GCAGCGGAGCAACAGAAGACGCTGAGAGAGTTCGTGGTGGTGATGGGCACTGAGCAGGACCGGGCCTGCTTCTTCCTCGA
GTCGGCTACCTGGGACTTGCAGATTGCGCTAGCGAGCTTTTATGAGGACAGAGGGGAAGAAGACATCATAACCATTTCAC
AGGCAACCCCCAGTTCAGTGTCCAGAGGCACAGCCCCTAGTGATAATAGAGTGACATCCTTTAGAGATCTCACTCATGAC
CAAGATGAGGATGAGGAAGAGGAGGAAGGCCAGAGGTTTTATGCCGGGGCCTCAGAGAGAAGTGGACAGCAGATTGTTGG
CCCTCCCAGAAAGAAAAGTTCCAATGAGCTGGTGGATGATCTCTTTAAAGGTGCCAAAGAGCATGGAGCTGTAGCTGTGG
AGCGAGTGACCAACAGACCTGGAGAGACCAGTACACCAAGACCATTTGCCGGAGATGGCTATGGCCTTGGGGCAGCACCA
GAGGAAGAGTCTGCTTATGTGGCAGGAGAAAAGAGACATCATTCCAACCAAGATGTTCATGTAGTACTGAAACTCTGCAA
GAGTGGATTCAGCCTGGATAATGGAGGACTCAGAAGCTACTGAGACCCATCCGATGCCCAGTTTCTGGAGTCTATCCACA
GAAGGGAGGTGCCAGCAGAGCTGTGGAGGCTAGCTCACAGTGGACAGGCGAACTTGGATATGGAGGAACATCAGGACGAG
GACTTTATGAAGTCCAAATAAGCCTTCAAAGCCTTCACTGGCGAGGGTCAGACACCGAGCAGCACTGCCCCCTAGGTGTT
GAGTACCATCTCTCCAGTCCAACTGGCAGAAAATGAAGCCAAAGCCAGCTCTTCCATCTTAATCGTCGAATCAGAGACTA
CCACAAACATCCAAATTCGGCTTGCAGACGGTGGGAGGCTGGTGCAGAAATTTAACCACAGCCACAGGATCAGCAACATC
CAACTCTTCATTGTGGATGCCCGGCCAGCCATGGCTGCCACCAGCTTTATCCTCATGACTACTTTCCCAAACAAAGAGCT
GGCTGACGAGAGCTGGACCCTGAAGGAAGCCAACCTGCTCAATGCTGCCATCATGCAG

ORF - retro_hsap_4050 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.34 %
Parental protein coverage: 98.92 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAAERQEALREFVAVTGAEEDRARFFLESAGWDLQIALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNR
AAE.Q..LREFV.V.G.E.DRA.FFLESA.WDLQIALASFYED.G.EDI.TISQATPSSVSRGTAPSDNR
RetrocopyAAEQQKTLREFVVVMGTEQDRACFFLESATWDLQIALASFYEDRGEEDIITISQATPSSVSRGTAPSDNR
ParentalVTSFRDLIHDQDEDEEEEEGQRFYAGGSERSGQQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSP
VTSFRDL.HDQDEDEEEEEGQRFYAG.SERSGQQIVGPPRKKS.NELVDDLFKGAKEHGAVAVERVT..P
RetrocopyVTSFRDLTHDQDEDEEEEEGQRFYAGASERSGQQIVGPPRKKSSNELVDDLFKGAKEHGAVAVERVTNRP
ParentalGETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLE
GETS.PRPFAG.GY.LGAAPEEESAYVAGEKR.HS.QDVHVVLKL.KSGFSLDNG.LRSY.DPS.AQFLE
RetrocopyGETSTPRPFAGDGYGLGAAPEEESAYVAGEKRHHSNQDVHVVLKLCKSGFSLDNGGLRSY*DPSDAQFLE
ParentalSIRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAENEA
SI.R.EVPAEL.RLAH.GQ.NLDME.H.DEDF.K.K.AFKAFTGEGQ...STAP.VLST.SP.Q.AENEA
RetrocopySIHRREVPAELWRLAHSGQANLDMEEHQDEDFMKSK*AFKAFTGEGQTPSSTAP*VLSTISPVQLAENEA
ParentalKASSSILIDESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPNKELADE
KASSSILI.ESE.TTNIQIRLADGGRLVQKFNHSHRIS.I.LFIVDARPAMAATSFILMTTFPNKELADE
RetrocopyKASSSILIVESETTTNIQIRLADGGRLVQKFNHSHRISNIQLFIVDARPAMAATSFILMTTFPNKELADE
ParentalSQTLKEANLLNAVIVQ
S.TLKEANLLNA.I.Q
RetrocopySWTLKEANLLNAAIMQ

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 .24 RPM 60 .91 RPM
bodymap2_adrenal 0 .51 RPM 50 .93 RPM
bodymap2_brain 0 .07 RPM 44 .25 RPM
bodymap2_breast 0 .14 RPM 48 .37 RPM
bodymap2_colon 0 .27 RPM 43 .95 RPM
bodymap2_heart 0 .20 RPM 33 .38 RPM
bodymap2_kidney 0 .85 RPM 34 .54 RPM
bodymap2_liver 0 .32 RPM 30 .12 RPM
bodymap2_lung 0 .18 RPM 42 .70 RPM
bodymap2_lymph_node 0 .26 RPM 40 .17 RPM
bodymap2_ovary 0 .48 RPM 60 .55 RPM
bodymap2_prostate 0 .48 RPM 62 .89 RPM
bodymap2_skeletal_muscle 0 .00 RPM 79 .46 RPM
bodymap2_testis 0 .26 RPM 59 .52 RPM
bodymap2_thyroid 0 .23 RPM 56 .12 RPM
bodymap2_white_blood_cells 0 .08 RPM 43 .27 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_4050 in 6 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 8:48424950..48425380
ENCFF002CJE POLR2A 8:48425025..48425269
ENCFF002CJZ POLR2A 8:48425121..48425259
ENCFF002CZC POLR2A 8:48425041..48425301
ENCFF002CZC POLR2A 8:48425055..48425595
ENCFF002CZD POLR2A 8:48425128..48425314
ENCFF002DAV POLR2A 8:48424987..48425531

EST - click to see more details

No EST(s) were mapped for retro_hsap_4050 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4050 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4050 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4050 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3324
Parental genes homology:
Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000088833 1 retrocopy
retro_hsap_4050 ,
Homo sapiens ENSG000001739601 retrocopy
retro_hsap_2025,
Homo sapiens ENSG000002151141 retrocopy
retro_hsap_3923,
Gorilla gorilla ENSGGOG000000135391 retrocopy
retro_ggor_2718,
Macropus eugenii ENSMEUG000000039402 retrocopies
retro_meug_1890, retro_meug_605,
Macaca mulatta ENSMMUG000000159941 retrocopy
retro_mmul_2337,
Mus musculus ENSMUSG000000274551 retrocopy
retro_mmus_2565,
Nomascus leucogenys ENSNLEG000000093411 retrocopy
retro_nleu_2800,
Otolemur garnettii ENSOGAG000000026302 retrocopies
retro_ogar_1144, retro_ogar_1609,
Pongo abelii ENSPPYG000000108511 retrocopy
retro_pabe_3324,
Pan troglodytes ENSPTRG000000131641 retrocopy
retro_ptro_2745,

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 = 0.65 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .15 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .29 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .32 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .30 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .30 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .19 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .20 RPM
FIN_HG00375 0 .27 RPM
FIN_HG00377 0 .33 RPM
FIN_HG00378 0 .28 RPM
GBR_HG00099 0 .38 RPM
GBR_HG00111 0 .56 RPM
GBR_HG00114 0 .21 RPM
GBR_HG00119 0 .31 RPM
GBR_HG00131 0 .32 RPM
GBR_HG00133 0 .17 RPM
GBR_HG00134 0 .28 RPM
GBR_HG00137 0 .38 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .35 RPM
TSI_NA20512 0 .23 RPM
TSI_NA20513 0 .58 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .65 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .23 RPM
TSI_NA20765 0 .46 RPM
TSI_NA20771 0 .23 RPM
TSI_NA20786 0 .31 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .21 RPM
YRI_NA19093 0 .10 RPM
YRI_NA19099 0 .27 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .15 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .32 RPM

Indel association:

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



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