RetrogeneDB ID:

retro_hsap_1765

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:47872704..47873031(+)
Located in intron of:ENSG00000136504
Retrocopy
information
Ensembl ID:ENSG00000235183
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SRP14
Ensembl ID:ENSG00000140319
Aliases:SRP14, ALURBP
Description:signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]


Retrocopy-Parental alignment summary:






>retro_hsap_1765
ATGGTGTTGTTGGAGAGTGAGCAGTTCCTGACGGAGCTGACCAGACTTTTCCAGAAGTGCTGGACATCGGGCAGCATCTA
TATCACCTTGAAGAAGTATGGTGGTGGAACCAAACCCGTTCCAAAGAAAGGTTCTGTGGAGGGCTTTGAGCCCTCAGACA
AGTGTCTGTTAAGAGCTATCGATGGGAAAAAGAAGGTCAGCACTGTGGTGAGCTCCAACCAAGTGAATAAGTTTCAGATG
GCTTATTCAAACCTACCGAGTGCTAACATGGATGGGCTGAAGAAAAGGGACAAAAAGAACAAAAGTAAGAAGACCAAAGC
AGCAGCA

ORF - retro_hsap_1765 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.36 %
Parental protein coverage: 80.88 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTV
MVLLESEQFLTELTRLFQKC.TSGS.YITLKKY.G.TKP.PKKG.VEGFEP.D.KCLLRA.DGKKK.STV
RetrocopyMVLLESEQFLTELTRLFQKCWTSGSIYITLKKYGGGTKPVPKKGSVEGFEPSD-KCLLRAIDGKKKVSTV
ParentalVSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKTKKTKAAA
VSS..VNKFQMAYSNL..ANMDGLKKRDKKNK.KKTKAAA
RetrocopyVSSNQVNKFQMAYSNLPSANMDGLKKRDKKNKSKKTKAAA

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 135 .77 RPM
bodymap2_adrenal 0 .04 RPM 159 .52 RPM
bodymap2_brain 0 .00 RPM 166 .35 RPM
bodymap2_breast 0 .02 RPM 158 .43 RPM
bodymap2_colon 0 .00 RPM 178 .45 RPM
bodymap2_heart 0 .07 RPM 113 .94 RPM
bodymap2_kidney 0 .00 RPM 182 .61 RPM
bodymap2_liver 0 .00 RPM 81 .56 RPM
bodymap2_lung 0 .00 RPM 160 .28 RPM
bodymap2_lymph_node 0 .00 RPM 148 .51 RPM
bodymap2_ovary 0 .06 RPM 182 .46 RPM
bodymap2_prostate 0 .00 RPM 224 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 70 .06 RPM
bodymap2_testis 0 .00 RPM 182 .71 RPM
bodymap2_thyroid 0 .00 RPM 225 .96 RPM
bodymap2_white_blood_cells 0 .00 RPM 135 .90 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1765 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1765 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_60203520 libraries739 libraries551 libraries16 libraries3 libraries

The graphical summary, for retro_hsap_1765 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_1765 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1765 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1181
Pongo abelii retro_pabe_1534
Macaca mulatta retro_mmul_1228
Parental genes homology:
Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000298892 retrocopies
retro_cfam_210, retro_cfam_40,
Choloepus hoffmanni ENSCHOG000000053212 retrocopies
retro_chof_212, retro_chof_2659,
Callithrix jacchus ENSCJAG000000209123 retrocopies
retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Cavia porcellus ENSCPOG000000089942 retrocopies
retro_cpor_1071, retro_cpor_462,
Dasypus novemcinctus ENSDNOG000000111473 retrocopies
retro_dnov_1303, retro_dnov_2164, retro_dnov_2599,
Echinops telfairi ENSETEG000000118701 retrocopy
retro_etel_1094,
Homo sapiens ENSG00000140319 3 retrocopies
retro_hsap_1765 , retro_hsap_811, retro_hsap_949,
Gorilla gorilla ENSGGOG000000099211 retrocopy
retro_ggor_665,
Myotis lucifugus ENSMLUG000000105315 retrocopies
retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta ENSMMUG000000160614 retrocopies
retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica ENSMODG000000292041 retrocopy
retro_mdom_1806,
Mustela putorius furoENSMPUG000000083241 retrocopy
retro_mputfur_376,
Nomascus leucogenys ENSNLEG000000024572 retrocopies
retro_nleu_246, retro_nleu_2831,
Otolemur garnettii ENSOGAG000000290702 retrocopies
retro_ogar_2839, retro_ogar_40,
Pongo abelii ENSPPYG000000063423 retrocopies
retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pan troglodytes ENSPTRG000000069113 retrocopies
retro_ptro_1181, retro_ptro_564, retro_ptro_656,
Tupaia belangeri ENSTBEG000000166371 retrocopy
retro_tbel_196,
Tarsius syrichta ENSTSYG000000094674 retrocopies
retro_tsyr_1283, retro_tsyr_1985, retro_tsyr_60, retro_tsyr_73,
Tursiops truncatus ENSTTRG000000000365 retrocopies
retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos ENSVPAG000000102821 retrocopy
retro_vpac_20,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 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 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 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 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .02 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 .07 RPM
TSI_NA20538 0 .05 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 .02 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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





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