RetrogeneDB ID:

retro_hsap_456

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:154386845..154387686(-)
Located in intron of:ENSG00000160712
Retrocopy
information
Ensembl ID:ENSG00000228264
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMD8
Ensembl ID:ENSG00000099341
Aliases:PSMD8, HEL-S-91n, HIP6, HYPF, Nin1p, Rpn12, S14, p31
Description:proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]


Retrocopy-Parental alignment summary:






>retro_hsap_456
GTGAACAGTGCAGCCGGCGCCTTGAGCTCCGGGCCCCTGGCGACCTAGGGCCCTGTCCTGCAGGCTGAGGACGGCAAGTA
CAAGCAACTCAAGGGCGAGTGGAACCGTAAAAGCCCCAATCTTAGCAAGTGCAGGGAAGAGCTGGGCTGCCTCAAGCTAG
TTCTTCTGGAGCTCAACTTCTTGCCAACCACAGGGACCAAGCTGACCAAACAGCAGCTCATTCTGGCCCGTGACATACTG
AAGATCGGGGCCAGTGGAGCATCCTATGCGAGGACATCCCCTCCTTCCAGCGCCACATGACCCAGCTCAAATGCTGCTAC
TTTGATTACAAGGAACAGCTTCCCCAGTCAGCCTACATGCACCAGCTCTTGGGCCTCAATCTCCTCTTCCTGCTGTCCCA
GAAGCGGGTGGCTGAGTTCCACATGGAGCTGGAGTGGCTGCCTGCCAAGGACATCCAGACCAATGTCTACACCAAAAACC
CTGTGTCCCTGGAGCAATACCTAATGGAGGGCAGCTACAACAAAGTGTTCCTGGCCAAGGGTAACATCCTCGCCAAGAGC
TACACCGTCTTCATCGACATCCTGCTTGACACTATCAGGGATGAGATGGCCGGGTGCATCAAGAAAGCCTATGAGAAAAT
CCCTTTTACCGAGGCCACCAGATCCTCTTCTTCAACACACCCAAAAAGATGACCGACTACACCAAGAAGTGAGGGTGGGT
CCCGGGCCCCAACAACTAATATAGTTTTGCCGGCCAGCAGCAGGAGCCAGAAGACACTACCATTCCCTCCACAGAACTGG
CCAAACAGGTCACCGAGTATGCCCGGCAGCTGGAGATGATC

ORF - retro_hsap_456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.87 %
Parental protein coverage: 97.91 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLTK
VN.AAG..SSGP.AT.G.VLQA..G.Y.QLKGEWNRKSPNLSKC.EELG.LKLVLLELNFLPTTGTKLTK
RetrocopyVNSAAGALSSGPLAT*GPVLQAEDGKYKQLKGEWNRKSPNLSKCREELGCLKLVLLELNFLPTTGTKLTK
ParentalQQLILARDILEIGA-QWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRVAE
QQLILARDIL.IGA.QWSIL..DIPSF.R.M.QLKC.YFDYKEQLP.SAYMHQLLGLNLLFLLSQ.RVAE
RetrocopyQQLILARDILKIGA<QWSILCEDIPSFQRHMTQLKCCYFDYKEQLPQSAYMHQLLGLNLLFLLSQKRVAE
ParentalFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEK
FH.ELE.LPAKDIQTNVY.K.PVSLEQYLMEGSYNKVFLAKGNI.A.SYT.FIDILLDTIRDE.AGCI.K
RetrocopyFHMELEWLPAKDIQTNVYTKNPVSLEQYLMEGSYNKVFLAKGNILAKSYTVFIDILLDTIRDEMAGCIKK
ParentalAYEKILFTEATR-ILFFNTPKKMTDYAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQL
AYEKI.FTEATR.ILFFNTPKKMTDY.KK.GWV.GPNN.YSFA.QQQ.PEDTTIPSTELAKQV.EYARQL
RetrocopyAYEKIPFTEATR<ILFFNTPKKMTDYTKK*GWVPGPNN*YSFAGQQQEPEDTTIPSTELAKQVTEYARQL
ParentalEMI
EMI
RetrocopyEMI

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 .28 RPM 87 .52 RPM
bodymap2_adrenal 0 .08 RPM 53 .12 RPM
bodymap2_brain 0 .07 RPM 40 .01 RPM
bodymap2_breast 0 .04 RPM 63 .66 RPM
bodymap2_colon 0 .00 RPM 43 .74 RPM
bodymap2_heart 0 .00 RPM 103 .40 RPM
bodymap2_kidney 0 .04 RPM 69 .51 RPM
bodymap2_liver 0 .00 RPM 64 .09 RPM
bodymap2_lung 0 .00 RPM 65 .14 RPM
bodymap2_lymph_node 0 .00 RPM 56 .28 RPM
bodymap2_ovary 0 .04 RPM 41 .37 RPM
bodymap2_prostate 0 .00 RPM 65 .68 RPM
bodymap2_skeletal_muscle 0 .11 RPM 195 .65 RPM
bodymap2_testis 0 .00 RPM 80 .94 RPM
bodymap2_thyroid 0 .23 RPM 64 .25 RPM
bodymap2_white_blood_cells 0 .00 RPM 56 .21 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_456 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_456 retrocopy
EST ID Start End Identity Match Mis-match Score
BE772765 154386920 154387307 99.8 384 0 382

TSS - click to see more details

No TSS is located nearby retro_hsap_456 retrocopy 5' end.

Lab - click to see more details

retro_hsap_456 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_456 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000099341 1 retrocopy
retro_hsap_456 ,
Monodelphis domestica ENSMODG000000131511 retrocopy
retro_mdom_58,
Nomascus leucogenys ENSNLEG000000168761 retrocopy
retro_nleu_878,
Pongo abelii ENSPPYG000000099311 retrocopy
retro_pabe_277,
Pan troglodytes ENSPTRG000000109261 retrocopy
retro_ptro_343,
Ictidomys tridecemlineatus ENSSTOG000000144641 retrocopy
retro_itri_10,

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 = 0.13 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 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 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 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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