RetrogeneDB ID:

retro_hsap_1278

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:70468207..70469013(-)
Located in intron of:ENSG00000150361
Retrocopy
information
Ensembl ID:ENSG00000232314
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_1278
CTAGTTAGGGTGAAGAAGGTGGGAAAGGTCTCCAAGGAGACCTATGCCAATTTGGAGGATTGGCCAACCAAATCCCAGAA
ATTAAGGAATTTGTGGAGCTTCCTCTCACACATCCTGAATGTTATGAAAATATGAATATCAAGTCCTCTAAGGAGATCAT
TCTCTATGGTCCACCTGACACAGCTAAAACCTTGTCGACCAAATTAGTTGCAAATCAAACCTCAGCCACTTTGTTGAGAT
TGATTGGCTTTGAACTTTTTTAGAATTACTGAGGTGATGGGCCCAATTTCATATGGGAATTGTTTCAAGTTGCTGAAAAT
ATGCACCTTCCATTGTGTTTATAGATGAAATTGATGGCATTAGGAAAAAAAGATATGACTCAAATTTTGGTGGTGAGAGA
TAAATTCAGCCAATAATGTTGGAACTGTTGAACCAGTTGGATGGATTTGGTTCAAGGGGAGATGTAAAAGTTATGGCCAC
AAGACAAATAGAAATTTTGGAGCTAGCGCTTATTAGACCAGATCGTATTGACTAGAAATTTGATTTCCCCCTACCTGATG
GAAAGACTAAGAAGCACATCTTTCAGATTTGCACAAGCAGGATTACGCTGGCCAATGATACAATCCTGGACAACTCCATC
ATGGCTAAAGATGACCTCTCTTGTACAGACCTCAAGGCAATGTGAATAGAAGTTGGTCTGGTGGCCATAAGAGAACATAG
AATAAAAGTAACACAATGACTTCAAAAAAATCGAAATAAATGTTCTTTATAAAAAACAGAAAGGCACCCCTTAGGGTCTC
TATCTC

ORF - retro_hsap_1278 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.61 %
Parental protein coverage: 61.59 %
Number of stop codons detected: 6
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLVTVMKVEKAPQETYADI-GGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKA
LV.V.KV.K...ETYA...GGL.NQI.EIKE.VELPLTHPE.YE.M.IK..K..ILYGPP.T.KTL..K.
RetrocopyLVRVKKVGKVSKETYANL<GGLANQIPEIKEFVELPLTHPECYENMNIKSSKEIILYGPPDTAKTLSTKL
ParentalVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAE-EHAPSIVFIDEIDAIGTKRYDSNSGGEREIQR
VANQTSAT.LR..G.EL...Y.GDGP....ELF.VAE...APSIVFIDEID.I..KRYDSN.GGER.IQ.
RetrocopyVANQTSATLLRLIGFELF*NY*GDGPNFIWELFQVAE<KYAPSIVFIDEIDGIRKKRYDSNFGGER*IQP
ParentalTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADD
.MLELLNQLDGF.SRGDVKV.MAT..IE.L..ALIRP.RID.K..FPLPD.KTKK.IFQI.TSR.TLA.D
RetrocopyIMLELLNQLDGFGSRGDVKV-MATRQIEILELALIRPDRID*KFDFPLPDGKTKKHIFQICTSRITLAND
ParentalVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVT-NEDFKKSKENVLYKKQEGTPEGLYL
..LD..IMAKDDLS..D.KA...E.GL.A.RE.R.KVT.N..FKK...NVLYKKQ.GTP.GLYL
RetrocopyTILDNSIMAKDDLSCTDLKAM*IEVGLVAIREHRIKVT>ND-FKKIEINVLYKKQKGTP*GLYL

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 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 0 .00 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_1278 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1278 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1278 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1278 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1278 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_874
Gorilla gorilla retro_ggor_1004
Pongo abelii retro_pabe_1059
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 ) 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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