RetrogeneDB ID:

retro_hsap_438

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:117075699..117076714(-)
Located in intron of:ENSG00000116815
Retrocopy
information
Ensembl ID:ENSG00000177173
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NAP1L4
Ensembl ID:ENSG00000205531
Aliases:NAP1L4, NAP1L4b, NAP2, NAP2L, hNAP2
Description:nucleosome assembly protein 1-like 4 [Source:HGNC Symbol;Acc:7640]


Retrocopy-Parental alignment summary:






>retro_hsap_438
ATGGCAGATAACAGTTTTTCAGATGGGGTTCCTTCAGATTTCGTGGAAGCTGCTAAAAATGCAAGTAAGACGGAAAAGCT
CACGGATCAGGTGATGCAGAATCCTGGAGTTTTGGCAGCTTTACAGGAGCGACTTGACAATGCCCCTCACACCCCTTCCA
GCTACATCGAAACTTTACCTAAAGCAGTAAAAAGAAGAATTAATGCATTGAAACAAATTCAGGTGAGATGCGCTCATATA
GAAGCCAAGTTCTATGAAGAAGTTCATGACTTGGAAAGAAAATATGCAGCATTATACCAGCCTCTCTTTGACGAGAGAAG
AGAATTTATCACCGGTGATGTTGAACCAACATCTGATATGGAATCAGAATGGCACCGTGAAAATGAAGAGGAGGAGAAAT
TGGCTGGAGACAGGAAAAATAAAGTAGTCATAACAGAAAAAGCAGCAGCAACAGCTGAAGAGCCAAATCCCAAAGGAATT
CCAGAGTTCTGGTTTACCATCTTTAGAAATGTAGATATGCTAAGTGAATTAGTCCAGGAATATGATGAACCAATCTTGAA
ATACCTGCAGGATATTAAAGTGAAGTTTTCTGACCCTGGACAGCCTATGTCTTTCATATTAAGAGTTCCACTTTCAACCC
AATGACTGCTTTGCCAACTCAGTCCTGACAAAAACCTGCAAGATGAAATCAGAACCAGATAAGGCTGATCCCTTTTCATT
TGCAGGTCCTGAGATCATGGACTGCGATGGGTGTACTATTGACTGGAAGAAAGGAAAGAATGTTACTGTCAAAACCATCA
AGAAAAAGCAGAAGCGTAAGGGTCCAGGCACTGTTAGAACAATTACCAAACAAGTATCCAATGAGTCATTTTTCAACTTC
TTCAATCCACTGAAAGCATCTGGGGACGGAGAATCACTGGATAAAGATTCTGAATTCGTATTAGCCTCTGATTTTGAAAT
TGGACACTTTTTCCGTGAGCGGACCACAGGCTGTGCTGTACTTCGCTGGGGAGGC

ORF - retro_hsap_438 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.68 %
Parental protein coverage: 89.87 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMADHSFSDGVPSDSVEAAKNASNTEKLTDQVMQNPRVLAALQERLDNVPHTPSSYIETLPKAVKRRINAL
MAD.SFSDGVPSD.VEAAKNAS.TEKLTDQVMQNP.VLAALQERLDN.PHTPSSYIETLPKAVKRRINAL
RetrocopyMADNSFSDGVPSDFVEAAKNASKTEKLTDQVMQNPGVLAALQERLDNAPHTPSSYIETLPKAVKRRINAL
ParentalKQLQVRCAHIEAKFYEEVHDLERKYAALYQPLFDKRREFITGDVEPT-DAESEWHSENEEEEKLAGDMKS
KQ.QVRCAHIEAKFYEEVHDLERKYAALYQPLFD.RREFITGDVEPT.D.ESEWH.ENEEEEKLAGD.K.
RetrocopyKQIQVRCAHIEAKFYEEVHDLERKYAALYQPLFDERREFITGDVEPTSDMESEWHRENEEEEKLAGDRKN
ParentalKVVVTEKAAATAEEPDPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQPMSFVL-EF
KVV.TEKAAATAEEP.PKGIPEFWFTIFRNVDMLSELVQEYDEPILK.LQDIKVKFSDPGQPMSF.L.EF
RetrocopyKVVITEKAAATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKYLQDIKVKFSDPGQPMSFIL>EF
ParentalHFEPNDYFTNSVLTKTYKMKSEPDKADPFSFEGPEIVDCDGCTIDWKKGKNVTVKTIKKKQKHKGRGTVR
HF.PND.F.NSVLTKT.KMKSEPDKADPFSF.GPEI.DCDGCTIDWKKGKNVTVKTIKKKQK.KG.GTVR
RetrocopyHFQPNDCFANSVLTKTCKMKSEPDKADPFSFAGPEIMDCDGCTIDWKKGKNVTVKTIKKKQKRKGPGTVR
ParentalTITKQVPNESFFNFFNPLKASGDGESLDEDSEFTLASDFEIGHFFRERIVPRAVLYFTG
TITKQV.NESFFNFFNPLKASGDGESLD.DSEF.LASDFEIGHFFRER....AVL...G
RetrocopyTITKQVSNESFFNFFNPLKASGDGESLDKDSEFVLASDFEIGHFFRERTTGCAVLRWGG

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 .16 RPM 67 .35 RPM
bodymap2_adrenal 0 .43 RPM 61 .14 RPM
bodymap2_brain 0 .07 RPM 100 .30 RPM
bodymap2_breast 0 .25 RPM 76 .32 RPM
bodymap2_colon 0 .12 RPM 67 .52 RPM
bodymap2_heart 0 .30 RPM 100 .32 RPM
bodymap2_kidney 0 .17 RPM 87 .83 RPM
bodymap2_liver 0 .11 RPM 33 .65 RPM
bodymap2_lung 0 .56 RPM 65 .95 RPM
bodymap2_lymph_node 0 .31 RPM 105 .84 RPM
bodymap2_ovary 0 .13 RPM 91 .64 RPM
bodymap2_prostate 0 .14 RPM 95 .07 RPM
bodymap2_skeletal_muscle 0 .00 RPM 141 .30 RPM
bodymap2_testis 0 .06 RPM 156 .31 RPM
bodymap2_thyroid 0 .19 RPM 94 .82 RPM
bodymap2_white_blood_cells 0 .10 RPM 98 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_438 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CHO POLR2A 1:117076681..117076999
ENCFF002CIO POLR2A 1:117076729..117077005

EST - click to see more details

1 EST(s) were mapped to retro_hsap_438 retrocopy
EST ID Start End Identity Match Mis-match Score
R19751 117075770 117076265 97.8 485 1 476

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_810371337 libraries472 libraries19 libraries0 libraries1 library

The graphical summary, for retro_hsap_438 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_438 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_438 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_192
Gorilla gorilla retro_ggor_423
Pongo abelii retro_pabe_288
Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001871093 retrocopies
retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Homo sapiens ENSG00000205531 1 retrocopy
retro_hsap_438 ,
Gorilla gorilla ENSGGOG000000132231 retrocopy
retro_ggor_423,
Nomascus leucogenys ENSNLEG000000108411 retrocopy
retro_nleu_1876,
Oryctolagus cuniculus ENSOCUG000000056241 retrocopy
retro_ocun_384,
Pongo abelii ENSPPYG000000029381 retrocopy
retro_pabe_288,
Pan troglodytes ENSPTRG000000287471 retrocopy
retro_ptro_192,

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 = 9.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 3 .94 RPM
CEU_NA11843 3 .64 RPM
CEU_NA11930 4 .69 RPM
CEU_NA12004 2 .13 RPM
CEU_NA12400 3 .33 RPM
CEU_NA12751 5 .05 RPM
CEU_NA12760 3 .50 RPM
CEU_NA12827 6 .41 RPM
CEU_NA12872 7 .02 RPM
CEU_NA12873 6 .29 RPM
FIN_HG00183 3 .43 RPM
FIN_HG00277 3 .55 RPM
FIN_HG00315 2 .62 RPM
FIN_HG00321 5 .26 RPM
FIN_HG00328 3 .46 RPM
FIN_HG00338 3 .41 RPM
FIN_HG00349 3 .27 RPM
FIN_HG00375 1 .79 RPM
FIN_HG00377 1 .34 RPM
FIN_HG00378 2 .51 RPM
GBR_HG00099 2 .03 RPM
GBR_HG00111 1 .68 RPM
GBR_HG00114 2 .89 RPM
GBR_HG00119 5 .20 RPM
GBR_HG00131 3 .48 RPM
GBR_HG00133 2 .19 RPM
GBR_HG00134 2 .75 RPM
GBR_HG00137 2 .56 RPM
GBR_HG00142 5 .36 RPM
GBR_HG00143 1 .31 RPM
TSI_NA20512 1 .27 RPM
TSI_NA20513 4 .74 RPM
TSI_NA20518 3 .80 RPM
TSI_NA20532 5 .41 RPM
TSI_NA20538 4 .51 RPM
TSI_NA20756 2 .53 RPM
TSI_NA20765 3 .19 RPM
TSI_NA20771 2 .18 RPM
TSI_NA20786 1 .49 RPM
TSI_NA20798 2 .65 RPM
YRI_NA18870 1 .90 RPM
YRI_NA18907 1 .66 RPM
YRI_NA18916 9 .07 RPM
YRI_NA19093 2 .76 RPM
YRI_NA19099 1 .12 RPM
YRI_NA19114 2 .41 RPM
YRI_NA19118 5 .26 RPM
YRI_NA19213 5 .57 RPM
YRI_NA19214 2 .09 RPM
YRI_NA19223 2 .77 RPM

Indel association:

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



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