RetrogeneDB ID:

retro_hsap_833

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:125937670..125938510(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254759
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NAP1L1
Ensembl ID:ENSG00000187109
Aliases:NAP1L1, NAP1, NAP1L, NRP
Description:nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]


Retrocopy-Parental alignment summary:






>retro_hsap_833
ATTAAATGTGCACAGATAGAAACCAAATTCTATGAGGAAGTTCACGATCTTGAAAGGAATATGCTGTTCTCTATCAGCCT
CTATTTGATAAGCGATTTGAGATTATTAATGAAATTTATGAACCCACAGAAGAACAATGTGAATGGTAACCAGATAAAGA
AGATGAGATTTCAGAGGAGTTGAAAGAAAAGGCCAAGATCGAAGATGAGAAAAAGGATGAAGAAAAAGAAGACCCCAAAG
AAATTCCTGAATTTTGGTTAACTGTTTCTAAGAATGTTGACTTGTTCAGTGATATGGTTCAACAACATGATGAACCTATT
CTGAAACACTTGAAAGATACTAAAGTGAAGCTCTCAGATGCTGACCAGCCTATGAATTTTGTCTTAGAATTTCACTTTGA
ACCCAATGAATATTTTACAAATGAAATGCTGTCAAAGACATACAGGATGAGGTCAGAACCAGATGATTCTGATCCCTTTT
CTTTTGATGGACCAGAAATTATGGGTTGCACAGGGTGCCAGATAGATTGGAAAAAAGGAAAGAATGTCACTTTGAAAACC
ATTAAGAAGAAGCAGAAACACAAGGGAAGTGGGACAGTTCATACTGTGACTAACACAGTTTCCAATGACTCTTTAATTTG
TTTGCCCCTCCTGAAGTTCCTGAGAGTGGAGATCTGGATGATGATGCTGAAATCCTTGCACAGACTTCAAAATAGGTCAC
TTTTTACGTGAGCGTATAATCCCAAGAGCAGTGTCATACTTTACTGGAGAAGCTATTGAAGTTGATGATGATGTTTATGA
TGAAGAAGGTGAAGAAGCGGATGAGGTAATGTTTACCAAA

ORF - retro_hsap_833 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.76 %
Parental protein coverage: 86.54 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVKCAQIEAKFYEEVHDLER-KYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEEDEISEELKEKAKIED
.KCAQIE.KFYEEVHDLER..YAVLYQPLFDKRFEIIN.IYEPTEE.CEW.PD.EDEISEELKEKAKIED
RetrocopyIKCAQIETKFYEEVHDLER<EYAVLYQPLFDKRFEIINEIYEPTEEQCEW*PDKEDEISEELKEKAKIED
ParentalEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFVLEFHFEPNEYF
EKKDEEKEDPK.IPEFWLTV.KNVDL.SDMVQ.HDEPILKHLKD.KVK.SDA.QPM.FVLEFHFEPNEYF
RetrocopyEKKDEEKEDPKEIPEFWLTVSKNVDLFSDMVQQHDEPILKHLKDTKVKLSDADQPMNFVLEFHFEPNEYF
ParentalTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKHKGRGTVRTVTKTVSN
TNE.L.KTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKHKG.GTV.TVT.TVSN
RetrocopyTNEMLSKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKHKGSGTVHTVTNTVSN
ParentalDS-FFNFFAPPEVPESGDLDDDAEAILA-ADFEIGHFLRERIIPRSVLYFTGEAIEDDDDDYDEEGEEAD
DS.F..F..P.EVPESGDLDDDAE.ILA..DF.IGHFLRERIIPR.V.YFTGEAIE.DDD.YDEEGEEAD
RetrocopyDS<FNLFAPP-EVPESGDLDDDAE-ILA<TDFKIGHFLRERIIPRAVSYFTGEAIEVDDDVYDEEGEEAD
ParentalEVMFTK
EVMFTK
RetrocopyEVMFTK

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 .76 RPM 622 .28 RPM
bodymap2_adrenal 0 .72 RPM 504 .31 RPM
bodymap2_brain 0 .66 RPM 437 .32 RPM
bodymap2_breast 0 .62 RPM 362 .05 RPM
bodymap2_colon 2 .22 RPM 672 .08 RPM
bodymap2_heart 0 .00 RPM 253 .43 RPM
bodymap2_kidney 0 .19 RPM 246 .02 RPM
bodymap2_liver 0 .06 RPM 51 .27 RPM
bodymap2_lung 0 .00 RPM 508 .09 RPM
bodymap2_lymph_node 0 .02 RPM 519 .96 RPM
bodymap2_ovary 1 .60 RPM 1239 .96 RPM
bodymap2_prostate 0 .28 RPM 612 .85 RPM
bodymap2_skeletal_muscle 0 .45 RPM 810 .63 RPM
bodymap2_testis 1 .92 RPM 534 .15 RPM
bodymap2_thyroid 0 .13 RPM 410 .84 RPM
bodymap2_white_blood_cells 0 .32 RPM 739 .34 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_833 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_833 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_114021062 libraries219 libraries492 libraries39 libraries17 libraries

The graphical summary, for retro_hsap_833 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_833 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_833 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_582
Gorilla gorilla retro_ggor_686
Parental genes homology:
Parental genes homology involve 16 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000209088 retrocopies
retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus ENSCJAG000000011151 retrocopy
retro_cjac_534,
Felis catus ENSFCAG000000002791 retrocopy
retro_fcat_1037,
Homo sapiens ENSG00000187109 3 retrocopies
retro_hsap_1199, retro_hsap_2696, retro_hsap_833 ,
Homo sapiens ENSG000002055311 retrocopy
retro_hsap_438,
Gorilla gorilla ENSGGOG000000038833 retrocopies
retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii ENSMEUG000000137022 retrocopies
retro_meug_1031, retro_meug_604,
Macaca mulatta ENSMMUG000000155831 retrocopy
retro_mmul_233,
Monodelphis domestica ENSMODG000000204564 retrocopies
retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furoENSMPUG000000174741 retrocopy
retro_mputfur_505,
Mus musculus ENSMUSG000000587991 retrocopy
retro_mmus_263,
Nomascus leucogenys ENSNLEG000000046824 retrocopies
retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Otolemur garnettii ENSOGAG000000103194 retrocopies
retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pan troglodytes ENSPTRG000000052404 retrocopies
retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Rattus norvegicus ENSRNOG000000038901 retrocopy
retro_rnor_150,
Vicugna pacos ENSVPAG000000072903 retrocopies
retro_vpac_435, retro_vpac_441, retro_vpac_601,

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 = 0.53 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .23 RPM
CEU_NA11930 0 .33 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 0 .19 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .36 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .15 RPM
FIN_HG00377 0 .25 RPM
FIN_HG00378 0 .21 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .24 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .25 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .11 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .53 RPM
TSI_NA20532 0 .31 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .20 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .17 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .30 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .31 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .29 RPM
YRI_NA19214 0 .07 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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