RetrogeneDB ID:

retro_hsap_2534

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:21:45466690..45466922(-)
Located in intron of:ENSG00000160218
Retrocopy
information
Ensembl ID:ENSG00000213440
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H2AFZ
Ensembl ID:ENSG00000164032
Aliases:H2AFZ, H2A.Z-1, H2A.z, H2A/z, H2AZ
Description:H2A histone family, member Z [Source:HGNC Symbol;Acc:4741]


Retrocopy-Parental alignment summary:






>retro_hsap_2534
ATGGCTGGCAGTAAGGTGGGAAAGGACTCCAGAAAGGCCAAGACAAAGGCGGTTTCCCGCTCGCAGAGCCGGCTTGCAGT
TCCCAGTGGGCCATATTCATCGACACCTGAAATGTAGGACGGCCAGTCATGGACGTGTGGGCGCGACTGCCGCTGTGTAC
AACACAGCCATCCTGGAGTACCTCGCTGCAGAGGGACTTGAACTGGCAGGAAATGCATCAAAAGACTTAAAG

ORF - retro_hsap_2534 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.75 %
Parental protein coverage: 60.94 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGGKAGKDSGKAKTKAVSRSQRAGLQFP-VGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLEL
MAG.K.GKDS.KAKTKAVSRSQ...L..P.VG.IHRHLK.RT.SHGRVGATAAVY..AILEYL.AE.LEL
RetrocopyMAGSKVGKDSRKAKTKAVSRSQ-SRLAVP>VGHIHRHLKCRTASHGRVGATAAVYNTAILEYLAAEGLEL
ParentalAGNASKDLK
AGNASKDLK
RetrocopyAGNASKDLK

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 70 .41 RPM
bodymap2_adrenal 0 .31 RPM 88 .94 RPM
bodymap2_brain 0 .00 RPM 67 .20 RPM
bodymap2_breast 0 .00 RPM 53 .89 RPM
bodymap2_colon 0 .10 RPM 152 .44 RPM
bodymap2_heart 0 .00 RPM 38 .99 RPM
bodymap2_kidney 0 .29 RPM 73 .21 RPM
bodymap2_liver 0 .00 RPM 25 .48 RPM
bodymap2_lung 0 .00 RPM 140 .26 RPM
bodymap2_lymph_node 0 .00 RPM 140 .67 RPM
bodymap2_ovary 0 .00 RPM 105 .29 RPM
bodymap2_prostate 0 .00 RPM 161 .04 RPM
bodymap2_skeletal_muscle 0 .00 RPM 42 .74 RPM
bodymap2_testis 0 .00 RPM 109 .37 RPM
bodymap2_thyroid 0 .00 RPM 92 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 114 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2534 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2534 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_1058011423 libraries394 libraries12 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_2534 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_2534 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2534 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1477
Parental genes homology:
Parental genes homology involve 24 parental genes, and 98 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009591 retrocopy
retro_amel_1183,
Canis familiaris ENSCAFG000000106152 retrocopies
retro_cfam_1000, retro_cfam_101,
Callithrix jacchus ENSCJAG000000152351 retrocopy
retro_cjac_91,
Echinops telfairi ENSETEG000000066132 retrocopies
retro_etel_137, retro_etel_54,
Homo sapiens ENSG000001059682 retrocopies
retro_hsap_1612, retro_hsap_890,
Homo sapiens ENSG00000164032 6 retrocopies
retro_hsap_1292, retro_hsap_2534 , retro_hsap_2581, retro_hsap_4073, retro_hsap_4113, retro_hsap_598,
Gorilla gorilla ENSGGOG000000278016 retrocopies
retro_ggor_1014, retro_ggor_137, retro_ggor_1616, retro_ggor_183, retro_ggor_2760, retro_ggor_720,
Loxodonta africana ENSLAFG000000284602 retrocopies
retro_lafr_1255, retro_lafr_269,
Macropus eugenii ENSMEUG000000136991 retrocopy
retro_meug_1457,
Microcebus murinus ENSMICG000000024693 retrocopies
retro_mmur_1056, retro_mmur_1159, retro_mmur_634,
Macaca mulatta ENSMMUG000000068347 retrocopies
retro_mmul_1049, retro_mmul_1320, retro_mmul_1593, retro_mmul_2368, retro_mmul_2448, retro_mmul_2465, retro_mmul_645,
Monodelphis domestica ENSMODG000000206862 retrocopies
retro_mdom_1506, retro_mdom_977,
Mustela putorius furoENSMPUG000000095192 retrocopies
retro_mputfur_1343, retro_mputfur_1529,
Mus musculus ENSMUSG000000378946 retrocopies
retro_mmus_2397, retro_mmus_2780, retro_mmus_2976, retro_mmus_3039, retro_mmus_3585, retro_mmus_953,
Nomascus leucogenys ENSNLEG000000136623 retrocopies
retro_nleu_2505, retro_nleu_2737, retro_nleu_2864,
Oryctolagus cuniculus ENSOCUG000000018882 retrocopies
retro_ocun_513, retro_ocun_728,
Otolemur garnettii ENSOGAG000000034198 retrocopies
retro_ogar_2276, retro_ogar_2377, retro_ogar_2722, retro_ogar_3255, retro_ogar_3396, retro_ogar_755, retro_ogar_866, retro_ogar_885,
Ochotona princeps ENSOPRG000000125821 retrocopy
retro_opri_404,
Pongo abelii ENSPPYG000000149577 retrocopies
retro_pabe_1070, retro_pabe_1901, retro_pabe_2374, retro_pabe_3343, retro_pabe_3367, retro_pabe_592, retro_pabe_668,
Pan troglodytes ENSPTRG000000163127 retrocopies
retro_ptro_1477, retro_ptro_1508, retro_ptro_2760, retro_ptro_2792, retro_ptro_441, retro_ptro_614, retro_ptro_884,
Rattus norvegicus ENSRNOG000000103069 retrocopies
retro_rnor_1136, retro_rnor_1202, retro_rnor_1605, retro_rnor_1933, retro_rnor_2155, retro_rnor_2413, retro_rnor_2494, retro_rnor_2908, retro_rnor_788,
Ictidomys tridecemlineatus ENSSTOG000000231941 retrocopy
retro_itri_1524,
Tupaia belangeri ENSTBEG0000000047815 retrocopies
retro_tbel_1289, retro_tbel_1290, retro_tbel_1320, retro_tbel_1925, retro_tbel_1959, retro_tbel_1972, retro_tbel_2304, retro_tbel_2526, retro_tbel_2685, retro_tbel_3575, retro_tbel_4077, retro_tbel_4308, retro_tbel_4369, retro_tbel_4451, retro_tbel_819,
Tarsius syrichta ENSTSYG000000094622 retrocopies
retro_tsyr_1715, retro_tsyr_971,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .10 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017