RetrogeneDB ID:

retro_hsap_3427

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:16171836..16172262(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000216364
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL42
Ensembl ID:ENSG00000198015
Aliases:MRPL42, L31MT, L42MT, MRP-L31, MRP-L42, MRP-S32, MRPL31, MRPS32, PTD007, RPML31, S32MT
Description:mitochondrial ribosomal protein L42 [Source:HGNC Symbol;Acc:14493]


Retrocopy-Parental alignment summary:






>retro_hsap_3427
ATGGCTGTAGCAGCAGTAAAATAGAGGACAGTAAAGCAAATTGTCTTGAAACATTTATTTCCAATGCAAAATGGAGCTTT
ATACTGTGTGTGTTATAAATCTATGTATTCTTCTCTACCTGATGACTATAATTGCAAAACAGAGCTTGCTGTGACTTCCA
ATGGCAGGAAGTGAGCCTGCTACCACTCTCCTGTGGACATTCCCTATGAATACACAAAACCCATCCTTCAACCACATCCT
GGGCACAATAATGAAGAAATACAAGATCAAGTGCTGAAAACCAGATTGGAAGAAAAAGGTGAACACCTTGAGCAAAGACC
CATGATAGAACAACTTAGCAAAATGTTCTTTAGTATTACACGCTGTTGGTATTCTCATGGACAGTATTAAAGATGTTGCA
AGAAACTAGATCTTCTAAAAGGCAGA

ORF - retro_hsap_3427 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.01 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAVAAVKWVMSKRTILKHLFPVQNGALYCVCHKSTYSPLPDDYNCNVELALTSDGRTIVCYHPSVDIPYE
MAVAAVK....K...LKHLFP.QNGALYCVC.KS.YS.LPDDYNC..ELA.TS.GR...CYH..VDIPYE
RetrocopyMAVAAVK*RTVKQIVLKHLFPMQNGALYCVCYKSMYSSLPDDYNCKTELAVTSNGRK*ACYHSPVDIPYE
ParentalHTKPIPRPDPVHNNEETHDQVLKTRLEEKVEHLEEGPMIEQLSKMFFTTKHRWYPHGRYHRCRKNLNPPK
.TKPI..P.P.HNNEE..DQVLKTRLEEK.EHLE..PMIEQLSKMFF.....WY.HG.Y.RC.K.L...K
RetrocopyYTKPILQPHPGHNNEEIQDQVLKTRLEEKGEHLEQRPMIEQLSKMFFSITRCWYSHGQY*RCCKKLDLLK
ParentalDR
.R
RetrocopyGR

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 26 .40 RPM
bodymap2_adrenal 0 .20 RPM 35 .88 RPM
bodymap2_brain 0 .00 RPM 24 .66 RPM
bodymap2_breast 0 .00 RPM 23 .85 RPM
bodymap2_colon 0 .00 RPM 31 .92 RPM
bodymap2_heart 0 .00 RPM 31 .31 RPM
bodymap2_kidney 0 .00 RPM 53 .54 RPM
bodymap2_liver 0 .00 RPM 24 .10 RPM
bodymap2_lung 0 .00 RPM 29 .64 RPM
bodymap2_lymph_node 0 .00 RPM 32 .82 RPM
bodymap2_ovary 0 .00 RPM 39 .34 RPM
bodymap2_prostate 0 .00 RPM 36 .75 RPM
bodymap2_skeletal_muscle 0 .00 RPM 18 .35 RPM
bodymap2_testis 0 .00 RPM 54 .73 RPM
bodymap2_thyroid 0 .06 RPM 33 .75 RPM
bodymap2_white_blood_cells 0 .00 RPM 32 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3427 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3427 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3427 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3427 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3427 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2327
Pongo abelii retro_pabe_2840
Parental genes homology:
Parental genes homology involve 19 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098321 retrocopy
retro_amel_403,
Bos taurus ENSBTAG000000027083 retrocopies
retro_btau_1395, retro_btau_346, retro_btau_775,
Callithrix jacchus ENSCJAG000000328254 retrocopies
retro_cjac_1541, retro_cjac_3684, retro_cjac_3966, retro_cjac_722,
Homo sapiens ENSG00000198015 3 retrocopies
retro_hsap_3427 , retro_hsap_3528, retro_hsap_3844,
Gorilla gorilla ENSGGOG000000227605 retrocopies
retro_ggor_1983, retro_ggor_2317, retro_ggor_2385, retro_ggor_2483, retro_ggor_2589,
Loxodonta africana ENSLAFG000000137791 retrocopy
retro_lafr_681,
Macaca mulatta ENSMMUG000000168053 retrocopies
retro_mmul_1751, retro_mmul_1850, retro_mmul_2210,
Nomascus leucogenys ENSNLEG000000056995 retrocopies
retro_nleu_1364, retro_nleu_1724, retro_nleu_1979, retro_nleu_493, retro_nleu_606,
Oryctolagus cuniculus ENSOCUG000000109287 retrocopies
retro_ocun_1321, retro_ocun_1378, retro_ocun_1497, retro_ocun_1716, retro_ocun_1717, retro_ocun_622, retro_ocun_686,
Ochotona princeps ENSOPRG000000109675 retrocopies
retro_opri_190, retro_opri_51, retro_opri_653, retro_opri_747, retro_opri_997,
Procavia capensis ENSPCAG000000037911 retrocopy
retro_pcap_179,
Pongo abelii ENSPPYG000000048337 retrocopies
retro_pabe_1286, retro_pabe_2368, retro_pabe_2840, retro_pabe_2914, retro_pabe_3031, retro_pabe_3054, retro_pabe_3552,
Pan troglodytes ENSPTRG000000227913 retrocopies
retro_ptro_1046, retro_ptro_2327, retro_ptro_2396,
Rattus norvegicus ENSRNOG000000427404 retrocopies
retro_rnor_1383, retro_rnor_633, retro_rnor_729, retro_rnor_920,
Sus scrofa ENSSSCG000000304784 retrocopies
retro_sscr_504, retro_sscr_505, retro_sscr_912, retro_sscr_946,
Ictidomys tridecemlineatus ENSSTOG0000002654412 retrocopies
retro_itri_1020, retro_itri_1132, retro_itri_1266, retro_itri_1285, retro_itri_1353, retro_itri_1695, retro_itri_1793, retro_itri_268, retro_itri_284, retro_itri_393, retro_itri_558, retro_itri_899,
Tarsius syrichta ENSTSYG000000063703 retrocopies
retro_tsyr_1296, retro_tsyr_2113, retro_tsyr_276,
Tursiops truncatus ENSTTRG000000033122 retrocopies
retro_ttru_1632, retro_ttru_416,
Vicugna pacos ENSVPAG000000076581 retrocopy
retro_vpac_336,

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 = 0.05 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 .05 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 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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