RetrogeneDB ID:

retro_hsap_2881

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:172143635..172144399(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236686
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BZW1
Ensembl ID:ENSG00000082153
Aliases:BZW1, BZAP45, Nbla10236
Description:basic leucine zipper and W2 domains 1 [Source:HGNC Symbol;Acc:18380]


Retrocopy-Parental alignment summary:






>retro_hsap_2881
CTAATGGCATCCATTCTTAATAGCCTTTATAATGAGAATTTGGTTAAAGAAGGGGTTTCAACAGCTTTTGCTGGAAAGCT
ATTTAAATCATGTATAAATGAAAAAGATATCAATGCAGTAACTGCAAGGAAAGTCAGCATGGATAACAGCCTGATGGAAC
TTTTTCCTGCCAATAAGCAAAGCGTTCAACACTTCACGAAGTATTTTACTGAGGCAGGCCTGAAAGAGCTTTCAGAATAT
GTTCGGAATCAGCAAACCATCAGAGCTTGTAAGGAGCTGCAGAAAGAACTTCAAGAACAGATGTCCCGTGGGGATCCATT
TAAGGTTATAATTTTATATGTCAAGGAGGAGATGAAAAAAAACAACATCCCAGAACCAGTTGTCATCGAAATAGTCTGGT
CAAATGTAATGAGCGCTGTGGAATGGAACAAAAGAGAGGAGATTGTAGCAGAGCAAGCCATCAAACACTTGAAGCAACAC
AGCCCTCTACTTGCTGCCTTTACTACTCAAAGTCAGTCTGAGCTGACCCTGTTACTGAAGATTCAGGAGTATTGCTATGA
CAACATTCATTTCATGAAAGCCTTCCGGAAAATAGTGGTGCTTTTTATAAAGCTGTAGTCCTGAGCAAAGAGCCCATTTT
GAAGTGGTATAAAGGTACACATGTTGCAAAGGGGAAGAGTGTTTTCCTTGAGCAAATGAAAAAGTTTGGAGAGTGGCTCA
AAAATGCTGAAGAAGAATCTGAATCTGAAGCTGAAGAAGGTGAC

ORF - retro_hsap_2881 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.76 %
Parental protein coverage: 56.98 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSMDNRLMELFPANKQSVEHFTKY
L.ASILNSLYNENLVKEGVS.AFA.KLFKS.INEKDINAV.A..RKVSMDN.LMELFPANKQSV.HFTKY
RetrocopyLMASILNSLYNENLVKEGVSTAFAGKLFKSCINEKDINAVTA--RKVSMDNSLMELFPANKQSVQHFTKY
ParentalFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMKKNNIPEPVVIGIVWSSVMS
FTEAGLKELSEYVRNQQTI.A.KELQKELQEQMSRGDPFK.IILYVKEEM...NIPEPVVI.IVWS.VMS
RetrocopyFTEAGLKELSEYVRNQQTIRACKELQKELQEQMSRGDPFKVIILYVKEEMXXXNIPEPVVIEIVWSNVMS
ParentalTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIHFMKAFQKIVVL-FYKAEV
.VEWNK.EE.VAEQAIKHLKQ.SPLLAAFTTQ.QSELTLLLKIQEYCYDNIHFMKAF.KIVVL.FYKA.V
RetrocopyAVEWNKREEIVAEQAIKHLKQHSPLLAAFTTQSQSELTLLLKIQEYCYDNIHFMKAFRKIVVL<FYKAVV
ParentalLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD
LS.EPILKWYK..HVAKGKSVFLEQMKKF.EWLKNAEEESESEAEEGD
RetrocopyLSKEPILKWYKGTHVAKGKSVFLEQMKKFGEWLKNAEEESESEAEEGD

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 .00 RPM 120 .58 RPM
bodymap2_adrenal 0 .00 RPM 64 .42 RPM
bodymap2_brain 0 .00 RPM 59 .73 RPM
bodymap2_breast 0 .00 RPM 87 .37 RPM
bodymap2_colon 0 .00 RPM 66 .50 RPM
bodymap2_heart 0 .00 RPM 42 .96 RPM
bodymap2_kidney 0 .00 RPM 85 .39 RPM
bodymap2_liver 0 .00 RPM 174 .84 RPM
bodymap2_lung 0 .00 RPM 125 .74 RPM
bodymap2_lymph_node 0 .00 RPM 85 .87 RPM
bodymap2_ovary 0 .00 RPM 103 .81 RPM
bodymap2_prostate 0 .00 RPM 79 .26 RPM
bodymap2_skeletal_muscle 0 .00 RPM 48 .11 RPM
bodymap2_testis 0 .00 RPM 137 .67 RPM
bodymap2_thyroid 0 .00 RPM 84 .72 RPM
bodymap2_white_blood_cells 0 .00 RPM 138 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2881 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2881 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_131776839 libraries718 libraries266 libraries4 libraries2 libraries

The graphical summary, for retro_hsap_2881 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_2881 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2881 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1949
Gorilla gorilla retro_ggor_1997
Macaca mulatta retro_mmul_1457
Parental genes homology:
Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000118781 retrocopy
retro_cfam_2150,
Choloepus hoffmanni ENSCHOG000000035438 retrocopies
retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus ENSCPOG000000104491 retrocopy
retro_cpor_331,
Homo sapiens ENSG00000082153 2 retrocopies
retro_hsap_2832, retro_hsap_2881 ,
Gorilla gorilla ENSGGOG000000162961 retrocopy
retro_ggor_1997,
Mustela putorius furoENSMPUG000000123441 retrocopy
retro_mputfur_1174,
Mus musculus ENSMUSG000000512233 retrocopies
retro_mmus_2499, retro_mmus_751, retro_mmus_990,
Nomascus leucogenys ENSNLEG000000069291 retrocopy
retro_nleu_621,
Pan troglodytes ENSPTRG000000127911 retrocopy
retro_ptro_1949,

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 = 0.04 RPM Legend:


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