RetrogeneDB ID:

retro_hsap_4148

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:32926055..32926372(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000223807
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BOLA3
Ensembl ID:ENSG00000163170
Aliases:BOLA3, MMDS2
Description:bolA homolog 3 (E. coli) [Source:HGNC Symbol;Acc:24415]


Retrocopy-Parental alignment summary:






>retro_hsap_4148
TGGAACCCTGCCCTTGTAGCTCCTCTCCACGCAGGATCTGCAGGCTTCCTCTTCTGCACTGTGTTCATTGAATGTTTGCC
TCCCAGACTGACGGGGAGCTCAAAGGGACCCAAATTCTCAAAGAGAAGTTTTCTGGAGCTACAGCTATCCAAGTCACTGA
CATTTCAGGAGGCTGTAGGTGATGTATAAAATCCAAATCAAACCAGAAGAATTTAAAGAAACAAGAACTGTCCCTCAGCA
CCAGATGATTAATCAGGCACTAAAAAAGGAAAATCAAAGGGATGCACAGATGGTGGGTATTTACCTCTGTCCCCAGA

ORF - retro_hsap_4148 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.14 %
Parental protein coverage: 96.26 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalWSPAAAAPLLRGIRG-LPLH---HRMFATQTEGELRVTQILKEKFPRATAIKVTDISGGCG-AMYEIKIE
W.PA..APL..G..G.LPL....H.MFA.QT.GEL..TQILKEKF..ATAI.VTDISGGC...MY.I.I.
RetrocopyWNPALVAPLHAGSAG<LPLLHCVH*MFASQTDGELKGTQILKEKFSGATAIQVTDISGGCR<VMYKIQIK
ParentalSEEFKEKRTVQQHQMVNQALKEE-IKEMHGLRIFTSVPK
.EEFKE.RTV.QHQM.NQALK.E.IK.MH....FTSVP.
RetrocopyPEEFKETRTVPQHQMINQALKKE>IKGMHRWWVFTSVPR

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 2 .92 RPM
bodymap2_adrenal 0 .04 RPM 7 .00 RPM
bodymap2_brain 0 .00 RPM 8 .32 RPM
bodymap2_breast 0 .06 RPM 7 .84 RPM
bodymap2_colon 0 .00 RPM 8 .02 RPM
bodymap2_heart 0 .00 RPM 15 .25 RPM
bodymap2_kidney 0 .00 RPM 15 .22 RPM
bodymap2_liver 0 .00 RPM 7 .50 RPM
bodymap2_lung 0 .00 RPM 3 .55 RPM
bodymap2_lymph_node 0 .00 RPM 7 .07 RPM
bodymap2_ovary 0 .04 RPM 4 .86 RPM
bodymap2_prostate 0 .00 RPM 8 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 6 .95 RPM
bodymap2_testis 0 .00 RPM 9 .62 RPM
bodymap2_thyroid 0 .00 RPM 10 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4148 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4148 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4148 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4148 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4148 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2786
Parental genes homology:
Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000178441 retrocopy
retro_cjac_1112,
Homo sapiens ENSG00000163170 3 retrocopies
retro_hsap_1959, retro_hsap_3383, retro_hsap_4148 ,
Gorilla gorilla ENSGGOG000000245054 retrocopies
retro_ggor_1423, retro_ggor_1424, retro_ggor_2290, retro_ggor_2786,
Macaca mulatta ENSMMUG000000152072 retrocopies
retro_mmul_1181, retro_mmul_2109,
Mus musculus ENSMUSG000000451601 retrocopy
retro_mmus_1648,
Nomascus leucogenys ENSNLEG000000003204 retrocopies
retro_nleu_1391, retro_nleu_1567, retro_nleu_2604, retro_nleu_971,
Oryctolagus cuniculus ENSOCUG000000166581 retrocopy
retro_ocun_51,
Pongo abelii ENSPPYG000000122852 retrocopies
retro_pabe_1618, retro_pabe_3461,
Pan troglodytes ENSPTRG000000120783 retrocopies
retro_ptro_1309, retro_ptro_2299, retro_ptro_2820,
Sorex araneus ENSSARG000000017541 retrocopy
retro_sara_83,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 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 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 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).



Copyright © RetrogeneDB 2014-2017