RetrogeneDB ID:

retro_hsap_3226

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:108120745..108121240(+)
Located in intron of:ENSG00000151422
Retrocopy
information
Ensembl ID:ENSG00000249921
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GNB2L1
Ensembl ID:ENSG00000204628
Aliases:GNB2L1, Gnb2-rs1, H12.3, HLC-7, PIG21, RACK1
Description:guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 [Source:HGNC Symbol;Acc:4399]


Retrocopy-Parental alignment summary:






>retro_hsap_3226
ACAGAGTGGGTGTCTTGTGTTCGCTTCTTGCCTAACAGCAGCAACCCTATCACTGTCTCCTGTAGCTGGGACAAGCTGGT
CAAGGTATGGAATCTGGCTAACTGCAAGCTGAAGACCAACCACATTGGCCACACAGGTTATCTGAACACTGTGACTATGT
CTCCAAATGGATCCCTCTGTGCATCTGGAGGCAAGGATGGCCAGGCCATGCTGTGGGATCTCAACGAAGGCAAACACCTT
TATATGCCAGATGGTGGGGGCATTATCAACACCCTGTGCTTCAGCCCCAACTGCTACTGGCTCTGTGCTGCCATGGGCCC
CAGCATCAAGATCTGGGACTTAGGGGTAAATATCATCGTAGATGAACTGAAGCAAGAAGTTATTAGTACTGGCAGCAAGG
CAGAACCACCCCAGTGTACCTCCCTGGCCTGGTCTGTTGGTGGTCATTTGTTTGCTGGCTACACAGACAACCTGGTGTGA
GTGTGGCAGGTGACA

ORF - retro_hsap_3226 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.35 %
Parental protein coverage: 60.81 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAM
.EWVSCVRF.PNSSNPI.VSC.WDKLVKVWNLANCKLKTNHIGHTGYLNTVT.SP.GSLCASGGKDGQAM
RetrocopyTEWVSCVRFLPNSSNPITVSCSWDKLVKVWNLANCKLKTNHIGHTGYLNTVTMSPNGSLCASGGKDGQAM
ParentalLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCT
LWDLNEGKHLY..DGG.IIN.LCFSPN.YWLCAA.GPSIKIWDL...IIVDELKQEVIST.SKAEPPQCT
RetrocopyLWDLNEGKHLYMPDGGGIINTLCFSPNCYWLCAAMGPSIKIWDLGVNIIVDELKQEVISTGSKAEPPQCT
ParentalSLAWSADGQTLFAGYTDNLVRVWQVT
SLAWS..G..LFAGYTDNLV.VWQVT
RetrocopySLAWSVGGH-LFAGYTDNLV*VWQVT

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 513 .45 RPM
bodymap2_adrenal 0 .00 RPM 658 .62 RPM
bodymap2_brain 0 .00 RPM 85 .13 RPM
bodymap2_breast 0 .00 RPM 401 .74 RPM
bodymap2_colon 0 .00 RPM 463 .35 RPM
bodymap2_heart 0 .00 RPM 190 .59 RPM
bodymap2_kidney 0 .02 RPM 324 .29 RPM
bodymap2_liver 0 .00 RPM 271 .95 RPM
bodymap2_lung 0 .00 RPM 646 .77 RPM
bodymap2_lymph_node 0 .00 RPM 944 .22 RPM
bodymap2_ovary 0 .00 RPM 799 .57 RPM
bodymap2_prostate 0 .00 RPM 899 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 638 .85 RPM
bodymap2_testis 0 .00 RPM 348 .69 RPM
bodymap2_thyroid 0 .00 RPM 312 .50 RPM
bodymap2_white_blood_cells 0 .00 RPM 986 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3226 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3226 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_147509915 libraries697 libraries207 libraries9 libraries1 library

The graphical summary, for retro_hsap_3226 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_3226 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3226 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2178
Gorilla gorilla retro_ggor_2194
Parental genes homology:
Parental genes homology involve 26 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000120081 retrocopy
retro_acar_185,
Ailuropoda melanoleuca ENSAMEG000000000041 retrocopy
retro_amel_1627,
Bos taurus ENSBTAG000000196481 retrocopy
retro_btau_1461,
Canis familiaris ENSCAFG000000248181 retrocopy
retro_cfam_1824,
Callithrix jacchus ENSCJAG000000187521 retrocopy
retro_cjac_2876,
Cavia porcellus ENSCPOG000000087241 retrocopy
retro_cpor_687,
Dipodomys ordii ENSDORG000000107351 retrocopy
retro_dord_117,
Equus caballus ENSECAG000000225673 retrocopies
retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus ENSEEUG000000087291 retrocopy
retro_eeur_368,
Echinops telfairi ENSETEG000000160243 retrocopies
retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens ENSG00000204628 1 retrocopy
retro_hsap_3226 ,
Gorilla gorilla ENSGGOG000000253671 retrocopy
retro_ggor_2194,
Macropus eugenii ENSMEUG000000110553 retrocopies
retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus ENSMLUG000000155071 retrocopy
retro_mluc_811,
Macaca mulatta ENSMMUG000000036041 retrocopy
retro_mmul_1956,
Monodelphis domestica ENSMODG000000040911 retrocopy
retro_mdom_1426,
Mustela putorius furoENSMPUG000000011482 retrocopies
retro_mputfur_1103, retro_mputfur_1111,
Mus musculus ENSMUSG000000203721 retrocopy
retro_mmus_3282,
Nomascus leucogenys ENSNLEG000000026041 retrocopy
retro_nleu_729,
Ornithorhynchus anatinus ENSOANG000000026001 retrocopy
retro_oana_127,
Otolemur garnettii ENSOGAG000000149242 retrocopies
retro_ogar_1257, retro_ogar_1591,
Pongo abelii ENSPPYG000000199391 retrocopy
retro_pabe_149,
Pan troglodytes ENSPTRG000000227341 retrocopy
retro_ptro_2178,
Rattus norvegicus ENSRNOG000000023903 retrocopies
retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus ENSSTOG000000070631 retrocopy
retro_itri_1752,
Tupaia belangeri ENSTBEG000000146612 retrocopies
retro_tbel_3897, retro_tbel_3899,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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