RetrogeneDB ID:

retro_hsap_292

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:204152133..204152550(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225522
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C12orf45
Ensembl ID:ENSG00000151131
Aliases:None
Description:chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628]


Retrocopy-Parental alignment summary:






>retro_hsap_292
ATAGAGGTCACCACAAGCCCCAGGCCAGCTCAAGCTCTGTGTTGTCCACCCAGGACTGCTACAGAGGGAGCCTTGGTGCC
TAAGGAGTGGCTGACGGTAGGGAACAACAGCCAAGGAGGTATATCAGACAGGTTGCTCATCAACTCCCAGCTTGATTCTA
GAAAGAACTCCACTCTCCAACCAGTCCAGACACAGAGGAGTCCCTTAGTGGACCAACGACAGACCTTTCTCCCACAGATG
GCCCAGGCACATGAAAAGCTAAGAAAATAAATGGCGGGTTCACCACCTGGTTGTTTCAGTATTGAAAATATTGATGGTTC
TCTTAGAAAAGTTATACAAATGGATATGGTCTTGTTTGAGATGAACCAGTCGAATTCAAAAGTAAAGAGTTCAGAATCTG
AGGATGAAGATGACAGC

ORF - retro_hsap_292 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.71 %
Parental protein coverage: 74.59 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEVHGKPK-ASPSCSSPTRDSSGVPVSKELLTAGSDGRGGIWDRLLINSQPKSRKTSTLQTVRIERSPLL
.EV...P..A...C..P.....G..V.KE.LT.G....GGI.DRLLINSQ..SRK.STLQ.V...RSPL.
RetrocopyIEVTTSPRPAQALCCPPRTATEGALVPKEWLTVGNNSQGGISDRLLINSQLDSRKNSTLQPVQTQRSPLV
ParentalDQVQTFLPQMARANEKLRKEMAAAPPGRFNIENIDGPHSKVIQMDVALFEMNQSDSKEVDSSEESSQDS
DQ.QTFLPQMA.A.EKLRK.MA..PPG.F.IENIDG...KVIQMD..LFEMNQS.SK...S..E...DS
RetrocopyDQRQTFLPQMAQAHEKLRK*MAGSPPGCFSIENIDGSLRKVIQMDMVLFEMNQSNSKVKSSESEDEDDS

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 4 .11 RPM
bodymap2_adrenal 0 .00 RPM 8 .72 RPM
bodymap2_brain 0 .00 RPM 2 .67 RPM
bodymap2_breast 0 .00 RPM 5 .43 RPM
bodymap2_colon 0 .00 RPM 5 .72 RPM
bodymap2_heart 0 .00 RPM 2 .27 RPM
bodymap2_kidney 0 .00 RPM 1 .92 RPM
bodymap2_liver 0 .00 RPM 3 .93 RPM
bodymap2_lung 0 .00 RPM 3 .32 RPM
bodymap2_lymph_node 0 .00 RPM 3 .97 RPM
bodymap2_ovary 0 .00 RPM 4 .14 RPM
bodymap2_prostate 0 .00 RPM 4 .28 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .95 RPM
bodymap2_testis 0 .00 RPM 6 .16 RPM
bodymap2_thyroid 0 .00 RPM 4 .09 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_292 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_292 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_292 retrocopy 5' end.

Lab - click to see more details

retro_hsap_292 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_292 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_240
Gorilla gorilla retro_ggor_331
Pongo abelii retro_pabe_382
Macaca mulatta retro_mmul_551
Parental genes homology:
Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000147281 retrocopy
retro_cjac_333,
Dasypus novemcinctus ENSDNOG000000172351 retrocopy
retro_dnov_2327,
Homo sapiens ENSG00000151131 1 retrocopy
retro_hsap_292 ,
Gallus gallus ENSGALG000000126941 retrocopy
retro_ggal_15,
Gorilla gorilla ENSGGOG000000272721 retrocopy
retro_ggor_331,
Macaca mulatta ENSMMUG000000171331 retrocopy
retro_mmul_551,
Nomascus leucogenys ENSNLEG000000065841 retrocopy
retro_nleu_2414,
Pongo abelii ENSPPYG000000048971 retrocopy
retro_pabe_382,
Pan troglodytes ENSPTRG000000053811 retrocopy
retro_ptro_240,
Sus scrofa ENSSSCG000000277922 retrocopies
retro_sscr_105, retro_sscr_153,
Tursiops truncatus ENSTTRG000000057141 retrocopy
retro_ttru_1381,

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 ) 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 .00 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 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 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 .00 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).





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