RetrogeneDB ID:

retro_hsap_3980

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:85591416..85592077(+)
Located in intron of:ENSG00000184672
Retrocopy
information
Ensembl ID:ENSG00000253137
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC2
Ensembl ID:ENSG00000161057
Aliases:PSMC2, MSS1, Nbla10058, S7
Description:proteasome (prosome, macropain) 26S subunit, ATPase, 2 [Source:HGNC Symbol;Acc:9548]


Retrocopy-Parental alignment summary:






>retro_hsap_3980
ACTGACATTGAGGCAGGGATGAAATTTGATGTGGAAGAATGTAAGTATTAAATTCATATTCCCATACTTTCTAAGATTGA
TCCAACAATTACCATGATGCCAGTGGAGTAAAAACCTGATGTCATATACAGTGATGTTGTTGGCTGTAGGGAACAGATTG
AGACATTGTAAGTAGTTGAAACCCCACTACTTCATCCAGAGAGATTTGTTAACCTTGGCATGGAGCCTCCCAAGAGTGTG
CTCTTTGGTCCACTAGGTGCAAGACACTCTGTGCTTAGGTGGTTGCTAAATAGGACTGATGCTTGCTTCATTGAGTTATT
GGATATTAACTTTTACAGAAATATATCTGCAAAGGGGCTGGAATGATTCATGAGCTCTTCCCAATGGCCAGAACAAGAAA
CGCCTGCCTTATCTTCTTTGATGAAACTGATGCTATTGGAAGAGCTCAGTTTGATGATGGTGCTGGAGGTGACAATGAAG
TACAGAGAAAAATGTGAGAACTAATTCATCAGTTGGATGGCTTTGACCCTCAAGGCAATATTAAGTGCTGATGGCCACTA
ACAGACCTGATACTTTGGATTCAGCACTGATGAAGCCAGGGAAATTGGATAGAAAGATTGAATTTAGTTTACCTGATCTA
GAGGGTCAGACTCACATCTTT

ORF - retro_hsap_3980 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.45 %
Parental protein coverage: 51.73 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERF
TDIE.GM...V...KY.IHIP...KIDPT.TMM.VE.KPDV.YSDV.GC.EQIE.L..VVETPLLHPERF
RetrocopyTDIEAGMKFDVEECKY*IHIPILSKIDPTITMMPVE*KPDVIYSDVVGCREQIETL*-VVETPLLHPERF
ParentalVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIR-VIGSELVQKYVGEGARMVRELFEMARTKKAC
VNLG.EPPK.V.LFGP.G.......R...NRTDACFI..VIG..L.QKY...GA.M..ELF.MART..AC
RetrocopyVNLGMEPPKSV-LFGPLGARHSV-LRWLLNRTDACFIE<VIGY*LLQKYICKGAGMIHELFPMARTRNAC
ParentalLIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIK-VLMATNRPDTLDPALMRPGRLDR
LIFFDE.DAIG.A.FDDGAGGDNEVQR.M.ELI.QLDGFDP.GNIK.VLMATNRPDTLD.ALM.PG.LDR
RetrocopyLIFFDETDAIGRAQFDDGAGGDNEVQRKM*ELIHQLDGFDPQGNIK<VLMATNRPDTLDSALMKPGKLDR
ParentalKIEFSLPDLEGRTHIF
KIEFSLPDLEG.THIF
RetrocopyKIEFSLPDLEGQTHIF

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 64 .82 RPM
bodymap2_adrenal 0 .00 RPM 91 .72 RPM
bodymap2_brain 0 .00 RPM 81 .81 RPM
bodymap2_breast 0 .00 RPM 80 .64 RPM
bodymap2_colon 0 .00 RPM 67 .33 RPM
bodymap2_heart 0 .00 RPM 54 .88 RPM
bodymap2_kidney 0 .00 RPM 87 .89 RPM
bodymap2_liver 0 .00 RPM 80 .73 RPM
bodymap2_lung 0 .00 RPM 42 .58 RPM
bodymap2_lymph_node 0 .00 RPM 56 .70 RPM
bodymap2_ovary 0 .02 RPM 83 .68 RPM
bodymap2_prostate 0 .00 RPM 66 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 89 .79 RPM
bodymap2_testis 0 .00 RPM 108 .65 RPM
bodymap2_thyroid 0 .00 RPM 120 .71 RPM
bodymap2_white_blood_cells 0 .00 RPM 62 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3980 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3980 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3980 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3980 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3980 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2702
Gorilla gorilla retro_ggor_2672
Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000057291 retrocopy
retro_etel_1316,
Homo sapiens ENSG00000161057 2 retrocopies
retro_hsap_2705, retro_hsap_3980 ,
Gorilla gorilla ENSGGOG000000091673 retrocopies
retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus ENSMLUG000000088531 retrocopy
retro_mluc_1642,
Macaca mulatta ENSMMUG000000034322 retrocopies
retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica ENSMODG000000172381 retrocopy
retro_mdom_868,
Mustela putorius furoENSMPUG000000182683 retrocopies
retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys ENSNLEG000000092742 retrocopies
retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii ENSOGAG000000051642 retrocopies
retro_ogar_2198, retro_ogar_2309,
Pongo abelii ENSPPYG000000178832 retrocopies
retro_pabe_2257, retro_pabe_2412,
Pan troglodytes ENSPTRG000000195532 retrocopies
retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta ENSTSYG000000006664 retrocopies
retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos ENSVPAG000000089211 retrocopy
retro_vpac_44,

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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