RetrogeneDB ID:

retro_hsap_2832

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:116364746..116365571(-)
Located in intron of:ENSG00000185565
Retrocopy
information
Ensembl ID:ENSG00000198406
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_2832
TCGGAGAGGAACAAGCTAGCTATGTTGACTGGTGTTCTTCTGGCTAATGGAACACTTAATGCATCCATTCTTAATAGCCT
TTATAATGAAAATTTGGTTAAAGAAGGAGTTTCAGCAGCTTTTGCTGTGAAGCTCTTTAAATCATGGATAAATGAAAAAG
ATATCAATGCAGTAGCTGCAAGTCTTCGGAAAGTCAGCATGGATAACAGACTGATGGAACTCTTTCCTGCCAATAAGCAA
AGTGTTGAACACTTCACAAAATATTTTACTGAGGCAGGCTTGAAAGAGCTTTCAGAATATGTTCGGAATCAGCAAACCAT
CGGAGCTCGTAAGGAGCTCCAGAAAGAACTTCAAGAACAGATGTCCCGTGGTGATCCATTTAAGGATATAATTTTATATG
TCAAGGAGGAGATGAAAAAAAACAACATCCCAGAGCCAGTTGTCATCGGAATAGTCTGGTCAAGTGTAATGAGCACTGTG
GAATGGAACAAAAAAGAGGAGCTTGTAGCAGAGCAAGCCATCAAGCACTTGAAGCAATACAGCCCTCTACTTGCTGCCTT
TACTACTCAAGGTCAGTCTGAGCTGACTCTGTTACTGAAGATTCAGGAGTATTGCTATGACAACATTCATTTCATGAAAG
CCTTCCAGAAAATAGTGGTGCTTTTTTATAAAGCTGAAGTCCTGAGCGAGGAGCCCATTTTGAAGTGGTATAAAGATGCA
CATGTTGCAAAGGGGAAGAGTGTTTTCCTTGAGCAAATGAAAAAGTTTGTAGAATGGCTCAAAAATGCTGAAGAAGAATC
TGAATCTGAAGCTGAAGAAGGTGAC

ORF - retro_hsap_2832 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.91 %
Parental protein coverage: 60.98 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSMDNR
SERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSMDNR
RetrocopySERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSMDNR
ParentalLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMKK
LMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEM..
RetrocopyLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMXX
ParentalNNIPEPVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIH
.NIPEPVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIH
RetrocopyXNIPEPVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIH
ParentalFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD
FMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD
RetrocopyFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD

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 .52 RPM 120 .58 RPM
bodymap2_adrenal 0 .23 RPM 64 .42 RPM
bodymap2_brain 0 .40 RPM 59 .73 RPM
bodymap2_breast 0 .31 RPM 87 .37 RPM
bodymap2_colon 0 .23 RPM 66 .50 RPM
bodymap2_heart 0 .02 RPM 42 .96 RPM
bodymap2_kidney 0 .21 RPM 85 .39 RPM
bodymap2_liver 0 .21 RPM 174 .84 RPM
bodymap2_lung 0 .12 RPM 125 .74 RPM
bodymap2_lymph_node 0 .09 RPM 85 .87 RPM
bodymap2_ovary 0 .50 RPM 103 .81 RPM
bodymap2_prostate 0 .05 RPM 79 .26 RPM
bodymap2_skeletal_muscle 0 .13 RPM 48 .11 RPM
bodymap2_testis 0 .66 RPM 137 .67 RPM
bodymap2_thyroid 0 .47 RPM 84 .72 RPM
bodymap2_white_blood_cells 0 .18 RPM 138 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2832 was not detected

EST - click to see more details

6 EST(s) were mapped to retro_hsap_2832 retrocopy
EST ID Start End Identity Match Mis-match Score
BF836509 201681826 201683116 98.1 410 7 399
BM790322 201681830 201683593 99.9 529 0 524
BP328875 201682756 201684918 99.7 575 2 569
CB129660 201681826 201683116 100 417 0 413
DA024628 201681826 201683624 100 566 0 563
DA660411 201681826 201683587 100 529 0 526

TSS - click to see more details

No TSS is located nearby retro_hsap_2832 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2832 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2832 has 0 orthologous retrocopies within eutheria group .

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 = 1.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .23 RPM
CEU_NA11930 0 .72 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .17 RPM
CEU_NA12760 0 .45 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .24 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 0 .36 RPM
FIN_HG00277 0 .30 RPM
FIN_HG00315 0 .22 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .11 RPM
FIN_HG00349 0 .57 RPM
FIN_HG00375 0 .42 RPM
FIN_HG00377 0 .23 RPM
FIN_HG00378 0 .34 RPM
GBR_HG00099 0 .44 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .24 RPM
GBR_HG00119 0 .19 RPM
GBR_HG00131 0 .26 RPM
GBR_HG00133 0 .17 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .29 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .29 RPM
TSI_NA20518 1 .08 RPM
TSI_NA20532 0 .24 RPM
TSI_NA20538 0 .41 RPM
TSI_NA20756 0 .26 RPM
TSI_NA20765 0 .27 RPM
TSI_NA20771 0 .31 RPM
TSI_NA20786 0 .26 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .61 RPM
YRI_NA18907 0 .21 RPM
YRI_NA18916 0 .17 RPM
YRI_NA19093 0 .23 RPM
YRI_NA19099 0 .56 RPM
YRI_NA19114 0 .24 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .22 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .26 RPM

Indel association:

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



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