RetrogeneDB ID:

retro_hsap_1228

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:98128003..98128577(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000271625
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA6
Ensembl ID:ENSG00000100902
Aliases:PSMA6, IOTA, PROS27, p27K
Description:proteasome (prosome, macropain) subunit, alpha type, 6 [Source:HGNC Symbol;Acc:9535]


Retrocopy-Parental alignment summary:






>retro_hsap_1228
TCCAGCACTGGTTTTGACCGCCACCTTATAATTTTTTCACCCAAGGTCCAGCTCTACCAAGTACAATATGCTTTTAAGGC
TATTAACCAGGGTGGCCTTACATCAGTAGCTGTCAGAAAGAAAGATTGTGCAGTAATTGTCACACACAAGATAGTACCTG
ACAAATTATTGGATTCCAGGACTCACTTATTCAAGATGACCAAAAACACTGGCCGTGTGATCACAGGAGTGACAGCTGAC
AGCAGATCCCGGGAACAGAGGGCGCAATATAAGGCAGCTAATTGCAAATACAAGTATGGCTATTAGATTCCTGTGGACAT
GCTGTGTAAAAGGAATTGCTGATATTACTCGGGTCTATACACAGAATGCTGAAATGAGGCCTCTTGGTTGTTGTATGATT
TTAATTAGTATATTTGAAGAACTAGGCCCTCGGGTGTACAAGTGTGATGCTGCAGGTTACTACTGTGGGTTTAAAGCCAC
TGCAGCAGGAGTTAAACAAGCCGAGTCAACCAGCTTCCTTGAAGTGAAGAAGAAATTTGCCTGGACATTTGAACACAGTG
GCAACCGCAATTAC

ORF - retro_hsap_1228 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.06 %
Parental protein coverage: 96.06 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLFKITE
SS.GFDRH..IFSP...LYQV.YAFKAINQGGLTSVAVR.KDCAVIVT.K.VPDKLLDS.T..HLFK.T.
RetrocopySSTGFDRHLIIFSPKVQLYQVQYAFKAINQGGLTSVAVRKKDCAVIVTHKIVPDKLLDSRT--HLFKMTK
ParentalNIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR-IADISQVYTQNAEMRPLGCCMILIGI
N.G.V.TG.TADSRS..QRA.Y.AAN.KYKYGY.IPVDMLCKR.IADI..VYTQNAEMRPLGCCMILI.I
RetrocopyNTGRVITGVTADSRSREQRAQYKAANCKYKYGY*IPVDMLCKR>IADITRVYTQNAEMRPLGCCMILISI
ParentalDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVEDSY
.EE.GP.VYKCD.AGYYCGFKATAAGVKQ.ESTSFLE..VKKKF.WTFE......Y
RetrocopyFEELGPRVYKCDAAGYYCGFKATAAGVKQAESTSFLE--VKKKFAWTFEHSGNRNY

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 32 .24 RPM
bodymap2_adrenal 0 .00 RPM 28 .02 RPM
bodymap2_brain 0 .00 RPM 18 .92 RPM
bodymap2_breast 0 .00 RPM 23 .64 RPM
bodymap2_colon 0 .00 RPM 18 .64 RPM
bodymap2_heart 0 .00 RPM 9 .91 RPM
bodymap2_kidney 0 .00 RPM 10 .96 RPM
bodymap2_liver 0 .00 RPM 8 .18 RPM
bodymap2_lung 0 .00 RPM 17 .99 RPM
bodymap2_lymph_node 0 .00 RPM 16 .03 RPM
bodymap2_ovary 0 .00 RPM 22 .79 RPM
bodymap2_prostate 0 .00 RPM 9 .30 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .68 RPM
bodymap2_testis 0 .00 RPM 30 .56 RPM
bodymap2_thyroid 0 .00 RPM 39 .17 RPM
bodymap2_white_blood_cells 0 .00 RPM 14 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1228 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1228 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1228 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1228 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1228 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_844
Parental genes homology:
Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000134092 retrocopies
retro_cfam_1581, retro_cfam_743,
Echinops telfairi ENSETEG000000048921 retrocopy
retro_etel_1775,
Felis catus ENSFCAG000000262761 retrocopy
retro_fcat_973,
Homo sapiens ENSG00000100902 2 retrocopies
retro_hsap_1228 , retro_hsap_4923,
Macropus eugenii ENSMEUG000000165371 retrocopy
retro_meug_1217,
Microcebus murinus ENSMICG000000000834 retrocopies
retro_mmur_104, retro_mmur_165, retro_mmur_752, retro_mmur_80,
Myotis lucifugus ENSMLUG000000102281 retrocopy
retro_mluc_822,
Macaca mulatta ENSMMUG000000165441 retrocopy
retro_mmul_343,
Mustela putorius furoENSMPUG000000162881 retrocopy
retro_mputfur_1089,
Mus musculus ENSMUSG000000210241 retrocopy
retro_mmus_654,
Otolemur garnettii ENSOGAG0000000849210 retrocopies
retro_ogar_1273, retro_ogar_1397, retro_ogar_1928, retro_ogar_1950, retro_ogar_2021, retro_ogar_2073, retro_ogar_2274, retro_ogar_2488, retro_ogar_2521, retro_ogar_3089,
Pan troglodytes ENSPTRG000000062642 retrocopies
retro_ptro_3297, retro_ptro_844,
Rattus norvegicus ENSRNOG000000071144 retrocopies
retro_rnor_1724, retro_rnor_1960, retro_rnor_854, retro_rnor_924,
Tupaia belangeri ENSTBEG0000001124117 retrocopies
retro_tbel_1304, retro_tbel_1415, retro_tbel_1789, retro_tbel_2028, retro_tbel_2466, retro_tbel_2519, retro_tbel_3227, retro_tbel_3280, retro_tbel_3535, retro_tbel_4181, retro_tbel_4183, retro_tbel_4357, retro_tbel_4465, retro_tbel_4495, retro_tbel_509, retro_tbel_602, retro_tbel_725,

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 = 0.07 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 .07 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 .03 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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