RetrogeneDB ID:

retro_hsap_1800

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:6830964..6831440(-)
Located in intron of:ENSG00000262943
Retrocopy
information
Ensembl ID:ENSG00000262503
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SPIC
Ensembl ID:ENSG00000166211
Aliases:SPIC, SPI-C
Description:Spi-C transcription factor (Spi-1/PU.1 related) [Source:HGNC Symbol;Acc:29549]


Retrocopy-Parental alignment summary:






>retro_hsap_1800
TTCAAAACTTACCTGGTTTTCATCAGTGATTGTACCCATGTCAGAGGAGATTCCAACTGCTATGGAATGTTGCTTACAGA
GGAATCTATTTATAATTGGAGAACTTTAATAAATAATGCTGCAGACTTCTATTTTGAAGGAACCATTCATTGATCTTTGT
GGAACATAACTGAAAGCCAGCTGGTGCAGTCTGCTGTTTTCCAGCAACAGGGAGGACAAGGCGGGAAGCTTCTCTGACTG
TTTGAATAACTTCACAAATCTCAGTATAATCCCAAGATGGCATCTGCATTCAGTAAGTAGATAAAACCAAAGGCAGTTTC
CAGTTTGTATCAAAAAATGAAGAAAAATTTGCCAAACTTTGAGGAATAAGAAAGGGCAATAGGAAGACCATGGTCTATCA
GAAAATGGCCAGGGAACTGAGGAATTATGGAAAAACTCAGGAAATCAACAAAATCTGGAGAAAGCTCATTTACCAA

ORF - retro_hsap_1800 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.12 %
Parental protein coverage: 64.11 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYRNYLALINHRPHVKGNSSCYGVLPTEEPVYNWRTVINSAADFYFEGNIHQSLQNITENQLVQPTLLQQK
...YL..I....HV.G.S.CYG.L.TEE..YNWRT.IN.AADFYFEG.IH.SL.NITE.QLVQ....QQ.
RetrocopyFKTYLVFISDCTHVRGDSNCYGMLLTEESIYNWRTLINNAADFYFEGTIH*SLWNITESQLVQSAVFQQQ
ParentalGGKGRKKLRLFEYLHESLYNPEMAS-CIQWVDKTKGIFQFVSKNKEKLAELWGKRKGNRKTMTYQKMARA
GG.G.K.L.LFE.LH.S.YNP.MAS.CIQ.VDKTKG.FQFVSKN.EK.A.L.G.RKGNRKTM.YQKMAR.
RetrocopyGGQGGKLL*LFE*LHKSQYNPKMAS<CIQ*VDKTKGSFQFVSKNEEKFAKL*GIRKGNRKTMVYQKMARE
ParentalLRNYGRSGEITKIRRKLTYQ
LRNYG...EI.KI.RKL.YQ
RetrocopyLRNYGKTQEINKIWRKLIYQ

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 .06 RPM 0 .00 RPM
bodymap2_adrenal 0 .08 RPM 7 .08 RPM
bodymap2_brain 0 .19 RPM 0 .00 RPM
bodymap2_breast 0 .12 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .15 RPM 0 .00 RPM
bodymap2_liver 0 .09 RPM 0 .85 RPM
bodymap2_lung 0 .12 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 1 .63 RPM
bodymap2_ovary 0 .35 RPM 0 .00 RPM
bodymap2_prostate 0 .14 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .09 RPM 0 .06 RPM
bodymap2_thyroid 0 .28 RPM 0 .06 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1800 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1800 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_624271824 libraries4 libraries0 libraries1 library0 libraries
TSS #2 TSS_624281821 libraries7 libraries0 libraries1 library0 libraries

The graphical summary, for retro_hsap_1800 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_1800 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1800 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1206
Gorilla gorilla retro_ggor_1324
Macaca mulatta retro_mmul_1245
Parental genes homology:
Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000099042 retrocopies
retro_btau_1281, retro_btau_1837,
Callithrix jacchus ENSCJAG000000019061 retrocopy
retro_cjac_3835,
Dasypus novemcinctus ENSDNOG000000044961 retrocopy
retro_dnov_759,
Equus caballus ENSECAG000000096141 retrocopy
retro_ecab_542,
Echinops telfairi ENSETEG000000042176 retrocopies
retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Homo sapiens ENSG00000166211 4 retrocopies
retro_hsap_1748, retro_hsap_1800 , retro_hsap_3135, retro_hsap_864,
Gorilla gorilla ENSGGOG000000245974 retrocopies
retro_ggor_1324, retro_ggor_1362, retro_ggor_2255, retro_ggor_703,
Loxodonta africana ENSLAFG000000156611 retrocopy
retro_lafr_912,
Myotis lucifugus ENSMLUG000000110521 retrocopy
retro_mluc_2169,
Macaca mulatta ENSMMUG000000208731 retrocopy
retro_mmul_1245,
Oryctolagus cuniculus ENSOCUG000000080701 retrocopy
retro_ocun_161,
Otolemur garnettii ENSOGAG000000151481 retrocopy
retro_ogar_1782,
Pongo abelii ENSPPYG000000048734 retrocopies
retro_pabe_1444, retro_pabe_1445, retro_pabe_2819, retro_pabe_686,
Pan troglodytes ENSPTRG000000053514 retrocopies
retro_ptro_1206, retro_ptro_1218, retro_ptro_3070, retro_ptro_598,
Rattus norvegicus ENSRNOG000000057201 retrocopy
retro_rnor_1519,
Ictidomys tridecemlineatus ENSSTOG000000154573 retrocopies
retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus ENSTTRG000000172051 retrocopy
retro_ttru_1708,

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 = 0.36 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .21 RPM
CEU_NA12751 0 .17 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .27 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .09 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .14 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .17 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .36 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .24 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .19 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .24 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .25 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .15 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .10 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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