RetrogeneDB ID:

retro_hsap_3535

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:151148798..151149517(+)
Located in intron of:ENSG00000120278
Retrocopy
information
Ensembl ID:ENSG00000213089
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDCL3
Ensembl ID:ENSG00000115539
Aliases:None
Description:phosducin-like 3 [Source:HGNC Symbol;Acc:28860]


Retrocopy-Parental alignment summary:






>retro_hsap_3535
ATGCAGGACCCCAACGCAGACACTGAGTGGAATGACATCTTACGCAAAAAGGGTTTCTTACCCGCCAAGGAAAGAATTGG
AAGAATTGGAAGAGGAGGCAGAAGAGGAGCAGCGCATCCTCCAGCAGTCAGTGGTGAAAACATATGAAGATATGACTTTG
GAAGAGCTGGAGGATCACGAAGGCGAGTTTAATGAGGAGGATGAATGTGCTATTGAAATGTACAGACAGCAGAGACTGGC
TGAGTGGAAAGCAACTAAACTGAAGAATAAATCTGGAAAAGTTTTGGAGATCTCAGGGAAGGATTATGTTCAAGAAGTTA
CCAAAGCTGGCGAGGGCTTGTGGGTCATCTTGCACCTTTACAAACAAGGAATTCCCCTCTGTGCCCTGATAAATCAGCAC
CTCAGTGGACTTGCCAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCATTTCAACAACCTGCATACCCAATTATACTGA
TAGGAATCTGCCCACGATATTTGTTTACCTGGAAGGAGATATCAAGGCTCAGTTTATTGGTCCTCTGAGTGTTTGGCGGC
ATGAACCTGACAAGAGATGAGTTGGAATGGAAACTGTCTGAATCTGGAGCAATTACGACAGACCTGGAGGAAAACCCTAA
GAAGCCGATTGAAGACGTGTTGCTCTCCTCAGTGCGGCGCTCTGTCCTCATGAAGAGGGACAGCGATTCCAAGGGTGAC

ORF - retro_hsap_3535 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.29 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQDPNADTEWNDILRKKGILP-PKESLKELEEEAEEEQRILQQSVVKTYEDMTLEELEDHEDEFNEEDER
MQDPNADTEWNDILRKKG.LP.P.........EAEEEQRILQQSVVKTYEDMTLEELEDHE.EFNEEDE.
RetrocopyMQDPNADTEWNDILRKKGFLP>PRXXXXXXXXEAEEEQRILQQSVVKTYEDMTLEELEDHEGEFNEEDEC
ParentalAIEMYRRRRLAEWKATKLKNKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHLSGLAR
AIEMYR..RLAEWKATKLKNK.G.VLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHLSGLAR
RetrocopyAIEMYRQQRLAEWKATKLKNKSGKVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHLSGLAR
ParentalKFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPL-VFGGMNLTRDELEWKLSESGAIMTDL
KFPDVKFIKAISTTCIPNY.DRNLPTIFVYLEGDIKAQFIGPL.VFGGMNLTRDELEWKLSESGAI.TDL
RetrocopyKFPDVKFIKAISTTCIPNYTDRNLPTIFVYLEGDIKAQFIGPL>VFGGMNLTRDELEWKLSESGAITTDL
ParentalEENPKKPIEDVLLSSVRRSVLMKRDSDSEGD
EENPKKPIEDVLLSSVRRSVLMKRDSDS.GD
RetrocopyEENPKKPIEDVLLSSVRRSVLMKRDSDSKGD

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 1 .45 RPM 17 .47 RPM
bodymap2_adrenal 1 .33 RPM 25 .83 RPM
bodymap2_brain 0 .26 RPM 11 .06 RPM
bodymap2_breast 0 .19 RPM 20 .95 RPM
bodymap2_colon 0 .29 RPM 33 .49 RPM
bodymap2_heart 0 .13 RPM 14 .07 RPM
bodymap2_kidney 0 .04 RPM 17 .47 RPM
bodymap2_liver 0 .06 RPM 4 .60 RPM
bodymap2_lung 0 .67 RPM 7 .77 RPM
bodymap2_lymph_node 0 .48 RPM 9 .85 RPM
bodymap2_ovary 0 .19 RPM 29 .26 RPM
bodymap2_prostate 0 .31 RPM 37 .01 RPM
bodymap2_skeletal_muscle 0 .18 RPM 18 .24 RPM
bodymap2_testis 0 .19 RPM 37 .12 RPM
bodymap2_thyroid 0 .06 RPM 21 .54 RPM
bodymap2_white_blood_cells 0 .06 RPM 15 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3535 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_3535 retrocopy
EST ID Start End Identity Match Mis-match Score
AW385983 151149111 151149293 99.1 102 0 99

TSS - click to see more details

No TSS is located nearby retro_hsap_3535 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3535 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3535 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2402
Parental genes homology:
Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000022261 retrocopy
retro_cfam_1740,
Callithrix jacchus ENSCJAG000000101603 retrocopies
retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii ENSDORG000000123971 retrocopy
retro_dord_702,
Erinaceus europaeus ENSEEUG000000002241 retrocopy
retro_eeur_506,
Homo sapiens ENSG00000115539 7 retrocopies
retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535 , retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus ENSMLUG000000164461 retrocopy
retro_mluc_1443,
Monodelphis domestica ENSMODG000000014891 retrocopy
retro_mdom_734,
Mus musculus ENSMUSG000000260781 retrocopy
retro_mmus_2284,
Nomascus leucogenys ENSNLEG000000143938 retrocopies
retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus ENSOCUG000000014692 retrocopies
retro_ocun_1035, retro_ocun_920,
Otolemur garnettii ENSOGAG000000151382 retrocopies
retro_ogar_1147, retro_ogar_2959,
Ochotona princeps ENSOPRG000000116002 retrocopies
retro_opri_1070, retro_opri_289,
Tursiops truncatus ENSTTRG000000062421 retrocopy
retro_ttru_1184,

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 = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .14 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .11 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .05 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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