RetrogeneDB ID:

retro_hsap_1612

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:93277040..93277425(-)
Located in intron of:ENSG00000185442
Retrocopy
information
Ensembl ID:ENSG00000258741
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H2AFV
Ensembl ID:ENSG00000105968
Aliases:H2AFV, H2A.Z-2, H2AV
Description:H2A histone family, member V [Source:HGNC Symbol;Acc:20664]


Retrocopy-Parental alignment summary:






>retro_hsap_1612
ATGGCCGGAGGCAAAGCTGGAAAGGACAGTGGGAAGGCCAAGGCTAAGGCAGTATCTCGCTCACAGAGAGCTGGGCTACA
GTTTCCTGTGGGCCGCATCCACAGACACTTGAAGACTCGCACCACAAGCCATGGAAGGGTGGGTGCCACTGCTGCCGTGC
ACAGGGCTGCGATTCCGGGGTACCTCACTGCAGAGGTGCTGGAGCTGGCAGGTAATGCTTCTAAGGGTCTCAAAGCAAAG
CGTATCACTCCGCGTCACTGGCAGCTTGCAGTCCGTGGTGATGAAGAGTTGGATTCTCTTATCAAGGCTACCACAGCTGG
GGGTGGCGTGATCCCCTCACATCCACAAATCTCTGACTGGAAAGAAGGGACAGCGGAAAACTGCT

ORF - retro_hsap_1612 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.7 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGGKAGKDSGKAKAKAVSRSQRAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELA
MAGGKAGKDSGKAKAKAVSRSQRAGLQFPVGRIHRHLKTRTTSHGRVGATAAV..AAI..YLTAEVLELA
RetrocopyMAGGKAGKDSGKAKAKAVSRSQRAGLQFPVGRIHRHLKTRTTSHGRVGATAAVHRAAIPGYLTAEVLELA
ParentalGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVI-PHIHKSLIGKKGQQKTA
GNASK.LK.KRITPRH.QLA.RGDEELDSLIKAT.AGGGVI.PHIHKSL.GKKGQ.KTA
RetrocopyGNASKGLKAKRITPRHWQLAVRGDEELDSLIKATTAGGGVI>PHIHKSLTGKKGQRKTA

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 .10 RPM 154 .41 RPM
bodymap2_adrenal 0 .00 RPM 119 .99 RPM
bodymap2_brain 0 .14 RPM 188 .76 RPM
bodymap2_breast 0 .04 RPM 180 .16 RPM
bodymap2_colon 0 .14 RPM 176 .58 RPM
bodymap2_heart 0 .06 RPM 195 .26 RPM
bodymap2_kidney 0 .17 RPM 126 .48 RPM
bodymap2_liver 0 .00 RPM 68 .42 RPM
bodymap2_lung 0 .23 RPM 140 .96 RPM
bodymap2_lymph_node 0 .02 RPM 126 .91 RPM
bodymap2_ovary 0 .29 RPM 193 .02 RPM
bodymap2_prostate 0 .36 RPM 179 .73 RPM
bodymap2_skeletal_muscle 0 .18 RPM 146 .72 RPM
bodymap2_testis 0 .40 RPM 129 .63 RPM
bodymap2_thyroid 0 .09 RPM 186 .28 RPM
bodymap2_white_blood_cells 0 .16 RPM 132 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1612 in 5 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 15:93277313..93277519
ENCFF002CFX POLR2A 15:93277302..93277514
ENCFF002DAE POLR2A 15:93277263..93277573
ENCFF002DBO POLR2A 15:93277216..93277600
ENCFF002DBP POLR2A 15:93277212..93277542

EST - click to see more details

No EST(s) were mapped for retro_hsap_1612 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_48093185 libraries209 libraries1144 libraries245 libraries46 libraries
TSS #2 TSS_480941059 libraries657 libraries107 libraries4 libraries2 libraries

The graphical summary, for retro_hsap_1612 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_1612 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1612 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1081
Gorilla gorilla retro_ggor_183
Parental genes homology:
Parental genes homology involve 23 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000169751 retrocopy
retro_btau_686,
Choloepus hoffmanni ENSCHOG000000008893 retrocopies
retro_chof_1967, retro_chof_2205, retro_chof_576,
Callithrix jacchus ENSCJAG000000119531 retrocopy
retro_cjac_3029,
Cavia porcellus ENSCPOG000000007691 retrocopy
retro_cpor_37,
Dipodomys ordii ENSDORG000000007935 retrocopies
retro_dord_100, retro_dord_12, retro_dord_171, retro_dord_195, retro_dord_291,
Erinaceus europaeus ENSEEUG000000158172 retrocopies
retro_eeur_359, retro_eeur_476,
Felis catus ENSFCAG000000102712 retrocopies
retro_fcat_373, retro_fcat_617,
Homo sapiens ENSG00000105968 2 retrocopies
retro_hsap_1612 , retro_hsap_890,
Homo sapiens ENSG000001640326 retrocopies
retro_hsap_1292, retro_hsap_2534, retro_hsap_2581, retro_hsap_4073, retro_hsap_4113, retro_hsap_598,
Myotis lucifugus ENSMLUG000000145002 retrocopies
retro_mluc_1492, retro_mluc_2122,
Mus musculus ENSMUSG000000411262 retrocopies
retro_mmus_1229, retro_mmus_1481,
Ornithorhynchus anatinus ENSOANG000000093782 retrocopies
retro_oana_55, retro_oana_87,
Oryctolagus cuniculus ENSOCUG0000000813310 retrocopies
retro_ocun_1226, retro_ocun_1336, retro_ocun_1456, retro_ocun_1596, retro_ocun_1938, retro_ocun_385, retro_ocun_389, retro_ocun_523, retro_ocun_601, retro_ocun_778,
Otolemur garnettii ENSOGAG000000251451 retrocopy
retro_ogar_3181,
Ochotona princeps ENSOPRG000000156043 retrocopies
retro_opri_315, retro_opri_538, retro_opri_942,
Pelodiscus sinensis ENSPSIG000000059311 retrocopy
retro_psin_62,
Pan troglodytes ENSPTRG000000191531 retrocopy
retro_ptro_1081,
Pteropus vampyrus ENSPVAG000000011093 retrocopies
retro_pvam_1284, retro_pvam_165, retro_pvam_213,
Rattus norvegicus ENSRNOG000000070265 retrocopies
retro_rnor_1410, retro_rnor_1815, retro_rnor_1935, retro_rnor_2102, retro_rnor_2310,
Sus scrofa ENSSSCG000000167381 retrocopy
retro_sscr_152,
Ictidomys tridecemlineatus ENSSTOG000000115331 retrocopy
retro_itri_148,
Tupaia belangeri ENSTBEG000000138405 retrocopies
retro_tbel_1155, retro_tbel_1295, retro_tbel_2747, retro_tbel_3214, retro_tbel_970,
Vicugna pacos ENSVPAG000000045071 retrocopy
retro_vpac_608,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .15 RPM
FIN_HG00378 0 .08 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .12 RPM
GBR_HG00134 0 .13 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .03 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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