RetrogeneDB ID:

retro_hsap_3416

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:4702699..4704010(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217385
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC1
Ensembl ID:ENSG00000100764
Aliases:PSMC1, P26S4, S4, p56
Description:proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]


Retrocopy-Parental alignment summary:






>retro_hsap_3416
GGTCAAAGTCAGAGTGGTGGTCACAGTCCTGGAGGTGGCAAGAAGGATGACAAGGACAAGAAAAAGAAATATGAACCTCC
TGTACCAACTGGAGTGGGGAAAAAGAAGAAAACAAAAGGATCAGATGTTGCCAGCAAACTGCCACTGGTGACACCTCACA
CTCAGTGCCCATTACAATTACTGAAGTTAGAGAGAATTAAGGACTATCTTCTCATGGAGGAAGAATTCAAAAGGAATCGG
GAACAAATGGAACCATTAGAAGAAAAGCAAGAGGAGGAAAGATCAAAGGTGGACGATCTGAGGGGACCCCGATGTCAGTA
GGAACCTTGGAAGAGATCAATGACAGTCATGCCATCGTGTCTACATCTGTGGGCTCAGGACACTACGCCAACATTCTTTC
ATTTGTAGACAAGGATCTGCTGGCAACTGGCTGCTCAGTCCTGCTCAATCACAAGGTGCATGCCATGAGAGGGGTGCTGA
TGGATGACGTGGATCCCCTGGTCACAGTGATGAAGGTGGAAAAGGTCCCCCAGGAGACCTATGCCAATACTGGGAGGTTG
GATAATCAAATTCAGGAAATTAAGGAATCTGTGGAGCTTCCTCTCACCCATGCTGAACATTATGAAGAGATGGGTATAAA
GCCTCCTAAGGGGGTCATTCTCTATGGTCCACCTGGCATAGTTAAAACCTTGCTAGCCAAAGCGGTAGCAAACCAAACCT
CAGCCACTTTCTTGAAAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTAGGTGATGGGCCCAAACTTGTACGGGAATTG
TTTCAAGTTGCTGGAGAACATGCACCATCCATCGTGTTTACTGATGAAACTGACGCCATTGGGACAAAAAGATATGACTC
AAATTCTGGTGGTGAGAGAGAAATTCAGCAAACAATGTTGGAACTGTTGAACCAGTTGGATGGATTTGATTCTAGGGGAG
ATGTGAAAGATATCATGACCACAAACTGAAGAGAAACTTTGGATCCAGCACTTATCAGACCAGGCCGCACTGGCAGGAAG
ATCAAGTTCCCCCTGCCTGATGAAAAGACTAAGAAGTGCATCTTTCAGATTCACACAAGCAGGATGATGCTGGCAGATGA
TGTAACCCTGGATGACTTGATCGTGGCTAAAGATGACCTCTCTGATGCTGACATCAAGGCAAATCTGTACAGAAGCTGGT
CTGATGGCCTTAAGAGAACGTAGAATGAAAGCAACAAATGAAGACTTCAAAAAATCTAAAGAAAATGTTCTTTATAAGAA
ACAGGAAGGCACCCCTGAGGGGCTGTCTCTC

ORF - retro_hsap_3416 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.66 %
Parental protein coverage: 99.77 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIKDY
GQSQSGGH.PGGGKKDDKDKKKKYEPPVPT.VGKKKK.TKG.D.ASKLPLVTPHTQC.L.LLKLERIKDY
RetrocopyGQSQSGGHSPGGGKKDDKDKKKKYEPPVPTGVGKKKK-TKGSDVASKLPLVTPHTQCPLQLLKLERIKDY
ParentalLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRG-TPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVD
LLMEEEF.RN.EQM.PLEEKQEEERSKVDDLRG.TPMSVGTLEEI..D.HAIVSTSVGS.HY..ILSFVD
RetrocopyLLMEEEFKRNREQMEPLEEKQEEERSKVDDLRG<TPMSVGTLEEI-NDSHAIVSTSVGSGHYANILSFVD
ParentalKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEY
KDLL..GCSVLLNHKVHA..GVLMDD.DPLVTVMKVEK.PQETYA..G.LDNQIQEIKESVELPLTH.E.
RetrocopyKDLLATGCSVLLNHKVHAMRGVLMDDVDPLVTVMKVEKVPQETYANTGRLDNQIQEIKESVELPLTHAEH
ParentalYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPS
YEEMGIKPPKGVILYGPPG..KTLLAKAVANQTSATFL.VVGSELIQKYLGDGPKLVRELF.VA.EHAPS
RetrocopyYEEMGIKPPKGVILYGPPGIVKTLLAKAVANQTSATFLKVVGSELIQKYLGDGPKLVRELFQVAGEHAPS
ParentalIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRK
IVF.DE.DAIGTKRYDSNSGGEREIQ.TMLELLNQLDGFDSRGDVK.IM.TN..ETLDPALIRPGR..RK
RetrocopyIVFTDETDAIGTKRYDSNSGGEREIQQTMLELLNQLDGFDSRGDVKDIMTTN*RETLDPALIRPGRTGRK
ParentalIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKA-ICTEAGLMALRERRMKVTNEDF
I.FPLPDEKTKK.IFQIHTSRM.LADDVTLDDLI.AKDDLS.ADIKA.ICTEAGLMALRERRMK.TNEDF
RetrocopyIKFPLPDEKTKKCIFQIHTSRMMLADDVTLDDLIVAKDDLSDADIKA>ICTEAGLMALRERRMKATNEDF
ParentalKKSKENVLYKKQEGTPEGLYL
KKSKENVLYKKQEGTPEGL.L
RetrocopyKKSKENVLYKKQEGTPEGLSL

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 .08 RPM 37 .95 RPM
bodymap2_adrenal 0 .00 RPM 37 .52 RPM
bodymap2_brain 0 .00 RPM 26 .25 RPM
bodymap2_breast 0 .00 RPM 31 .85 RPM
bodymap2_colon 0 .00 RPM 23 .22 RPM
bodymap2_heart 0 .00 RPM 33 .49 RPM
bodymap2_kidney 0 .00 RPM 24 .42 RPM
bodymap2_liver 0 .00 RPM 23 .28 RPM
bodymap2_lung 0 .00 RPM 20 .43 RPM
bodymap2_lymph_node 0 .00 RPM 18 .07 RPM
bodymap2_ovary 0 .00 RPM 35 .16 RPM
bodymap2_prostate 0 .00 RPM 28 .53 RPM
bodymap2_skeletal_muscle 0 .00 RPM 61 .89 RPM
bodymap2_testis 2 .85 RPM 32 .69 RPM
bodymap2_thyroid 0 .00 RPM 58 .19 RPM
bodymap2_white_blood_cells 0 .00 RPM 23 .72 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3416 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3416 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3416 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3416 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3416 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2309
Parental genes homology:
Parental genes homology involve 14 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000175102 retrocopies
retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni ENSCHOG000000135951 retrocopy
retro_chof_1954,
Callithrix jacchus ENSCJAG000000177017 retrocopies
retro_cjac_1152, retro_cjac_1537, retro_cjac_2417, retro_cjac_2433, retro_cjac_4219, retro_cjac_661, retro_cjac_678,
Dasypus novemcinctus ENSDNOG000000064581 retrocopy
retro_dnov_2162,
Homo sapiens ENSG00000100764 10 retrocopies
retro_hsap_1090, retro_hsap_1278, retro_hsap_2080, retro_hsap_2658, retro_hsap_2810, retro_hsap_2873, retro_hsap_3323, retro_hsap_3416 , retro_hsap_3793, retro_hsap_975,
Gorilla gorilla ENSGGOG000000106208 retrocopies
retro_ggor_1004, retro_ggor_1298, retro_ggor_1629, retro_ggor_1954, retro_ggor_1993, retro_ggor_2309, retro_ggor_780, retro_ggor_858,
Macropus eugenii ENSMEUG000000015261 retrocopy
retro_meug_623,
Microcebus murinus ENSMICG000000167337 retrocopies
retro_mmur_1039, retro_mmur_1063, retro_mmur_1245, retro_mmur_1577, retro_mmur_216, retro_mmur_839, retro_mmur_983,
Macaca mulatta ENSMMUG000000229901 retrocopy
retro_mmul_255,
Nomascus leucogenys ENSNLEG0000001701310 retrocopies
retro_nleu_1123, retro_nleu_1163, retro_nleu_1589, retro_nleu_1625, retro_nleu_1669, retro_nleu_2318, retro_nleu_2625, retro_nleu_429, retro_nleu_616, retro_nleu_706,
Oryctolagus cuniculus ENSOCUG000000062314 retrocopies
retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii ENSOGAG000000323432 retrocopies
retro_ogar_3014, retro_ogar_367,
Pongo abelii ENSPPYG000000259489 retrocopies
retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pan troglodytes ENSPTRG000000066239 retrocopies
retro_ptro_1530, retro_ptro_1904, retro_ptro_1944, retro_ptro_2153, retro_ptro_2321, retro_ptro_2573, retro_ptro_672, retro_ptro_742, retro_ptro_874,

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 = 0.03 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 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 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 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 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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