RetrogeneDB ID:

retro_hsap_4684

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:53852378..53852804(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235916
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPS18C
Ensembl ID:ENSG00000163319
Aliases:None
Description:mitochondrial ribosomal protein S18C [Source:HGNC Symbol;Acc:16633]


Retrocopy-Parental alignment summary:






>retro_hsap_4684
GCTATGGTTGCTGTTTGCGGTGGTCTAGGGAGGAAGAAGTTGACACACCTGGTAACGGCTGCTGTCAGCCTTACACATCC
CGGGACTCCCATGGTGCTTTCGAGAAGGGGTTATTCACAATATAAACAGGTATCCAGCATTGAGGACCTGCCCACTCCAA
TGGAAAACCCTTATAAAGAATCTCTTAAGAAGTGTGTCTTGTGTGGAAAGCATGTAAATTATAAGAATGCACAGCTTTTG
TCCCAGTTTGTTTCTCCATTTACTGGATGCATTTATGGAAGGCACGTTACAGGTCTTTGTGGGAAGAAACAGAAAGAAAT
CACAAAAGCAATTAAGAGAGCTCAAATAATGGGGTTTATGCCAGTTACATACAAAGATCCTGCATATCTCAAGGACCCTA
AAGTTTGTAACATCAGATATCAGGAA

ORF - retro_hsap_4684 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.73 %
Parental protein coverage: 98.59 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAVVAVCGGLGRKKLTHLVTAAVSLTHPGTHTVLWRRGCSQ--QVSSNEDLPISMENPYKEPLKKCILCGK
A.VAVCGGLGRKKLTHLVTAAVSLTHPGT..VL.RRG.SQ..QVSS.EDLP..MENPYKE.LKKC.LCGK
RetrocopyAMVAVCGGLGRKKLTHLVTAAVSLTHPGTPMVLSRRGYSQYKQVSSIEDLPTPMENPYKESLKKCVLCGK
ParentalHVDYKNVQLLSQFVSPFTGCIYGRHITGLCGKKQKEITKAIKRAQIMGFMPVTYKDPAYLKDPKVCNIRY
HV.YKN.QLLSQFVSPFTGCIYGRH.TGLCGKKQKEITKAIKRAQIMGFMPVTYKDPAYLKDPKVCNIRY
RetrocopyHVNYKNAQLLSQFVSPFTGCIYGRHVTGLCGKKQKEITKAIKRAQIMGFMPVTYKDPAYLKDPKVCNIRY
ParentalRE
.E
RetrocopyQE

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 .02 RPM 9 .86 RPM
bodymap2_adrenal 0 .00 RPM 19 .67 RPM
bodymap2_brain 0 .00 RPM 12 .42 RPM
bodymap2_breast 0 .00 RPM 13 .64 RPM
bodymap2_colon 0 .00 RPM 16 .53 RPM
bodymap2_heart 0 .00 RPM 8 .47 RPM
bodymap2_kidney 0 .00 RPM 17 .72 RPM
bodymap2_liver 0 .00 RPM 11 .55 RPM
bodymap2_lung 0 .00 RPM 6 .86 RPM
bodymap2_lymph_node 0 .00 RPM 8 .90 RPM
bodymap2_ovary 0 .00 RPM 17 .14 RPM
bodymap2_prostate 0 .00 RPM 13 .15 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .04 RPM
bodymap2_testis 0 .00 RPM 19 .57 RPM
bodymap2_thyroid 0 .00 RPM 15 .63 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4684 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4684 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4684 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4684 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4684 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2908
Pongo abelii retro_pabe_70
Macaca mulatta retro_mmul_2494
Parental genes homology:
Parental genes homology involve 20 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000181553 retrocopies
retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus ENSCJAG000000052863 retrocopies
retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus ENSCPOG000000091981 retrocopy
retro_cpor_178,
Dasypus novemcinctus ENSDNOG000000183262 retrocopies
retro_dnov_1030, retro_dnov_152,
Homo sapiens ENSG00000163319 5 retrocopies
retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684 , retro_hsap_969,
Gorilla gorilla ENSGGOG000000086032 retrocopies
retro_ggor_1173, retro_ggor_2908,
Macropus eugenii ENSMEUG000000109722 retrocopies
retro_meug_104, retro_meug_1113,
Myotis lucifugus ENSMLUG000000170571 retrocopy
retro_mluc_2360,
Mus musculus ENSMUSG000000168332 retrocopies
retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys ENSNLEG000000091194 retrocopies
retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps ENSOPRG000000041132 retrocopies
retro_opri_1041, retro_opri_966,
Pongo abelii ENSPPYG000000258672 retrocopies
retro_pabe_1276, retro_pabe_70,
Pan troglodytes ENSPTRG000000162333 retrocopies
retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus ENSPVAG000000064392 retrocopies
retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus ENSRNOG000000021783 retrocopies
retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii ENSSHAG000000070841 retrocopy
retro_shar_718,
Ictidomys tridecemlineatus ENSSTOG000000079891 retrocopy
retro_itri_1231,
Tupaia belangeri ENSTBEG000000125053 retrocopies
retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta ENSTSYG000000129241 retrocopy
retro_tsyr_649,
Tursiops truncatus ENSTTRG000000048972 retrocopies
retro_ttru_144, retro_ttru_1721,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 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 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .03 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 .02 RPM

Indel association:

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





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