RetrogeneDB ID:

retro_hsap_4236

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:26880175..26880547(-)
Located in intron of:ENSG00000120159
Retrocopy
information
Ensembl ID:ENSG00000232466
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3B
Ensembl ID:ENSG00000132475
Aliases:H3F3B, H3.3B
Description:H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]


Retrocopy-Parental alignment summary:






>retro_hsap_4236
GTGGCTCCTACAAAGCAGACTGCTTGCACATTAACTGGTGGTAAAGCATCCAGGAAGCAACTGACTACAAAGGCTGCTTA
CAAGAGTGCACCCTCTCCTGGAGTGGTGAAGAAACCTCATTGTTACAGGCCTGGTACTGTGGCACTCCATGAAATCAGTT
GTTTCTGGAAGTCCACTGAACTTCTGAATCACACACTTCCCTTCCACGGTCTGGCTTGAGAAATTGCTCAGGACTTCAAA
TCAGACCAGTGCGTCCAGAGCGCAGCTATTGGTGCTTTGCGGGAGGCAAGTGAGGCCTATCTGGTTGTCCTTTTTGAAGA
CACCAGCCTGTGTGCTGTCCATGCCAAATGTATAACAATTATGCCAAAAGAC

ORF - retro_hsap_4236 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.39 %
Parental protein coverage: 91.18 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
.A.TKQTA...TGGKA.RKQL.TKAA.KSAPS.G.VKKPH.YRPGTVAL.EI....KSTELL...LPF..
RetrocopyVAPTKQTACTLTGGKASRKQLTTKAAYKSAPSPGVVKKPHCYRPGTVALHEISCFWKSTELLNHTLPFHG
ParentalLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD
L..EIAQDFK.D...QSAAIGAL.EASEAYLV.LFEDT.LCA.HAK..TIMPKD
RetrocopyLA*EIAQDFKSDQCVQSAAIGALREASEAYLVVLFEDTSLCAVHAKCITIMPKD

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 .02 RPM 358 .42 RPM
bodymap2_adrenal 0 .14 RPM 566 .78 RPM
bodymap2_brain 0 .05 RPM 541 .14 RPM
bodymap2_breast 0 .00 RPM 323 .45 RPM
bodymap2_colon 0 .02 RPM 361 .41 RPM
bodymap2_heart 0 .04 RPM 91 .05 RPM
bodymap2_kidney 0 .00 RPM 326 .19 RPM
bodymap2_liver 0 .00 RPM 114 .76 RPM
bodymap2_lung 0 .00 RPM 619 .46 RPM
bodymap2_lymph_node 0 .00 RPM 265 .57 RPM
bodymap2_ovary 0 .00 RPM 1184 .97 RPM
bodymap2_prostate 0 .00 RPM 568 .46 RPM
bodymap2_skeletal_muscle 0 .00 RPM 113 .47 RPM
bodymap2_testis 0 .00 RPM 496 .18 RPM
bodymap2_thyroid 0 .02 RPM 1081 .08 RPM
bodymap2_white_blood_cells 0 .00 RPM 627 .57 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4236 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4236 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4236 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4236 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4236 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2879
Parental genes homology:
Parental genes homology involve 11 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG0000001270210 retrocopies
retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus ENSDNOG000000248432 retrocopies
retro_dnov_1624, retro_dnov_775,
Equus caballus ENSECAG000000069041 retrocopy
retro_ecab_916,
Equus caballus ENSECAG000000169481 retrocopy
retro_ecab_266,
Homo sapiens ENSG00000132475 11 retrocopies
retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236 , retro_hsap_911,
Homo sapiens ENSG000001630415 retrocopies
retro_hsap_2825, retro_hsap_2889, retro_hsap_3102, retro_hsap_3214, retro_hsap_4800,
Latimeria chalumnae ENSLACG000000041181 retrocopy
retro_lcha_104,
Loxodonta africana ENSLAFG000000080833 retrocopies
retro_lafr_837, retro_lafr_959, retro_lafr_99,
Microcebus murinus ENSMICG000000021392 retrocopies
retro_mmur_36, retro_mmur_371,
Mustela putorius furoENSMPUG000000045554 retrocopies
retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Pongo abelii ENSPPYG000000086361 retrocopy
retro_pabe_2662,

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 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 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .12 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 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017