RetrogeneDB ID:

retro_hsap_4157

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:37836036..37836393(+)
Located in intron of:ENSG00000255872
Retrocopy
information
Ensembl ID:ENSG00000232454
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPS10
Ensembl ID:ENSG00000048544
Aliases:MRPS10, MRP-S10, PNAS-122
Description:mitochondrial ribosomal protein S10 [Source:HGNC Symbol;Acc:14502]


Retrocopy-Parental alignment summary:






>retro_hsap_4157
CACGGTAAGGCTGTATTGGACAGTTATGAATATTTTGCTGTGCTTGATGCTAAAGAACTTGGTATCTCTATTAAAGTACA
CGAACCTCCAAGGAAAATAGAGCGATTTACTCTTCTCATATCAGTGCATATTTATAAGAAGCACGGAGTTCAGTATGAAA
TGAGAACACTTTACAGATGTTTAGAGTTAGAACATCTAACTGGAAGCACAGCAGATGTCTACGTGGAATATATTCAGCGA
AACTTACCTGAAAGGGTTGCCATGGAAGTAACAAAGACACAATTAGAACAGTTACCAGAACACATCAAGGAGCCAATCTG
GGAAACACTATCAGAAGAAAAAGAAGAAAGCAAGTCT

ORF - retro_hsap_4157 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.96 %
Parental protein coverage: 59.2 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLQSVHIYKKHRVQYEMRTLYRCLELEHLTGST
H.KAVLDSYEYFAVL.AKELGISIKVHEPPRKIERFTLL.SVHIYKKH.VQYEMRTLYRCLELEHLTGST
RetrocopyHGKAVLDSYEYFAVLDAKELGISIKVHEPPRKIERFTLLISVHIYKKHGVQYEMRTLYRCLELEHLTGST
ParentalADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS
ADVY.EYIQRNLPE.VAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS
RetrocopyADVYVEYIQRNLPERVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS

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 34 .67 RPM
bodymap2_adrenal 0 .10 RPM 40 .14 RPM
bodymap2_brain 0 .12 RPM 39 .80 RPM
bodymap2_breast 0 .06 RPM 48 .70 RPM
bodymap2_colon 0 .33 RPM 43 .02 RPM
bodymap2_heart 0 .02 RPM 52 .23 RPM
bodymap2_kidney 0 .00 RPM 43 .20 RPM
bodymap2_liver 0 .02 RPM 32 .51 RPM
bodymap2_lung 0 .00 RPM 24 .07 RPM
bodymap2_lymph_node 0 .00 RPM 25 .99 RPM
bodymap2_ovary 0 .12 RPM 46 .07 RPM
bodymap2_prostate 0 .02 RPM 40 .22 RPM
bodymap2_skeletal_muscle 0 .00 RPM 33 .34 RPM
bodymap2_testis 0 .06 RPM 52 .22 RPM
bodymap2_thyroid 0 .32 RPM 54 .65 RPM
bodymap2_white_blood_cells 0 .00 RPM 34 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4157 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4157 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4157 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4157 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4157 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2826
Pongo abelii retro_pabe_3456
Parental genes homology:
Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG000000020811 retrocopy
retro_dord_412,
Homo sapiens ENSG00000048544 1 retrocopy
retro_hsap_4157 ,
Gorilla gorilla ENSGGOG000000128081 retrocopy
retro_ggor_2532,
Microcebus murinus ENSMICG000000113791 retrocopy
retro_mmur_321,
Macaca mulatta ENSMMUG000000146611 retrocopy
retro_mmul_48,
Mus musculus ENSMUSG000000347291 retrocopy
retro_mmus_1654,
Nomascus leucogenys ENSNLEG000000048001 retrocopy
retro_nleu_1385,
Oryctolagus cuniculus ENSOCUG000000166971 retrocopy
retro_ocun_1141,
Pongo abelii ENSPPYG000000166131 retrocopy
retro_pabe_3456,
Pan troglodytes ENSPTRG000000181691 retrocopy
retro_ptro_2826,
Rattus norvegicus ENSRNOG000000226091 retrocopy
retro_rnor_2284,
Ictidomys tridecemlineatus ENSSTOG000000270161 retrocopy
retro_itri_1183,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 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 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .15 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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