RetrogeneDB ID:

retro_hsap_2458

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:20834767..20835285(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225803
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPS11
Ensembl ID:ENSG00000181991
Aliases:MRPS11, HCC-2
Description:mitochondrial ribosomal protein S11 [Source:HGNC Symbol;Acc:14050]


Retrocopy-Parental alignment summary:






>retro_hsap_2458
AGGGTCATGGCCAGGATGCTGGTGCAGACCATCCACACAGGCACCCAGAAGATCCAAGACATTGAGGCCAAGCAGAACAT
TGAAGAGAAGATGGTAGCTCCCAGCTACACCAGCTTTAGCATTTACCGTCCCATTACAAAAGAAAAAAGCTCTCTGAGGT
GGGCAGGAAAGAAATTTGAGGAGATCCCAACTGCACACATTAGAGCATCCTACAACAACACACAGATCCAGGTAATCTCT
GCCACTAATCAGCCCCTTGCCCATACTTCCTGTGGCACAGAGGAATTTCTGAATGCCAAGAAGGGCACAGGCATTAATGC
ACAGACAACAGGCATAGCAGCCGTGACAAAAGCTGCAGGAAAGGGTGTTACCCACATCTGAGTTGTGGTGAAAGGCCAGG
GGCCAGGACACCTGTCTGCCATCCAGGGACTGACCATGGGGGGCCTGGAAGTGATCTCAATCACAGCAACACCCCCATCC
CACACAATGGCTCCTGCCCCAAGAAGGCTCCGAGGCTG

ORF - retro_hsap_2458 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.39 %
Parental protein coverage: 88.66 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRVVARTPAGTICTGARQLQDAAAKQKVEQN-AAPSHTKFSIYPPIPGEESSLRWAGKKFEEIPIAHIKAS
RV.AR....TI.TG....QD..AKQ..E....APS.T.FSIY.PI..E.SSLRWAGKKFEEIP.AHI.AS
RetrocopyRVMARMLVQTIHTGTQKIQDIEAKQNIEEKMVAPSYTSFSIYRPITKEKSSLRWAGKKFEEIPTAHIRAS
ParentalHNNTQIQVVSASNEPLAFASCGTEGFRNAKKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSA
.NNTQIQV.SA.N.PLA..SCGTE.F.NAKKGTGI.AQT.GIAA...A..KGV.HI.VVVKG.GPG.LSA
RetrocopyYNNTQIQVISATNQPLAHTSCGTEEFLNAKKGTGINAQTTGIAAVTKAAGKGVTHI*VVVKGQGPGHLSA
ParentalMHGLIMGGLEVISIT-DNTPIPHNGCRPRKARKL
..GL.MGGLEVISIT..NTPIPHNG..P.KA..L
RetrocopyIQGLTMGGLEVISIT<SNTPIPHNGSCPKKAPRL

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 12 .24 RPM
bodymap2_adrenal 0 .04 RPM 17 .03 RPM
bodymap2_brain 0 .00 RPM 14 .72 RPM
bodymap2_breast 0 .00 RPM 17 .16 RPM
bodymap2_colon 0 .00 RPM 14 .15 RPM
bodymap2_heart 0 .00 RPM 17 .15 RPM
bodymap2_kidney 0 .00 RPM 16 .96 RPM
bodymap2_liver 0 .00 RPM 18 .21 RPM
bodymap2_lung 0 .00 RPM 5 .85 RPM
bodymap2_lymph_node 0 .00 RPM 15 .28 RPM
bodymap2_ovary 0 .00 RPM 9 .60 RPM
bodymap2_prostate 0 .00 RPM 13 .34 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .64 RPM
bodymap2_testis 0 .02 RPM 20 .10 RPM
bodymap2_thyroid 0 .00 RPM 23 .86 RPM
bodymap2_white_blood_cells 0 .00 RPM 10 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2458 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2458 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2458 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2458 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2458 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1531
Pan troglodytes retro_ptro_1419
Macaca mulatta retro_mmul_637
Parental genes homology:
Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000130122 retrocopies
retro_cjac_2601, retro_cjac_2989,
Felis catus ENSFCAG000000149671 retrocopy
retro_fcat_282,
Homo sapiens ENSG00000181991 1 retrocopy
retro_hsap_2458 ,
Gorilla gorilla ENSGGOG000000151521 retrocopy
retro_ggor_1531,
Macaca mulatta ENSMMUG000000136591 retrocopy
retro_mmul_637,
Nomascus leucogenys ENSNLEG000000114411 retrocopy
retro_nleu_1902,
Ochotona princeps ENSOPRG000000082471 retrocopy
retro_opri_540,
Pongo abelii ENSPPYG000000067512 retrocopies
retro_pabe_1808, retro_pabe_2583,
Pan troglodytes ENSPTRG000000074201 retrocopy
retro_ptro_1419,

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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