RetrogeneDB ID:

retro_hsap_2067

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:52929115..52929406(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000269776
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DPPA5
Ensembl ID:ENSG00000203909
Aliases:DPPA5, ESG1
Description:developmental pluripotency associated 5 [Source:HGNC Symbol;Acc:19201]


Retrocopy-Parental alignment summary:






>retro_hsap_2067
CTGAAAGATCCAGAGGTGCTCCAGGTCCAGATGCAGCTGCTGGAAGCCATGTTTGGCCCAGACTGATCTCAAATCCCTTA
CATCGAGCAGGTGAGCAAGGTCATGCTCGTGCTGAAGGCTCTGGAGTCTTCAGACCTCACCGAGGTTGTCGGTTACGGCT
TCTATTTATACAAGTGCCAGACCAAGTGGATGCCCCAGTCCATGGCTGAGTGGCACTGCCAGTGCCAGGAGCGAGGGATG
CTCAAACTTGTGGAAAGCATGAATGCCGTCAAACTACGCCCTTGGGTGAAG

ORF - retro_hsap_2067 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.32 %
Parental protein coverage: 83.62 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLKDPEVFQVQTRLLKAIFGPDGSRIPYIEQVSKAMLELKALESSDLTEVVVYGSYLYKLRTKWMLQSMAE
LKDPEV.QVQ..LL.A.FGPD.S.IPYIEQVSK.ML.LKALESSDLTEVV.YG.YLYK..TKWM.QSMAE
RetrocopyLKDPEVLQVQMQLLEAMFGPD*SQIPYIEQVSKVMLVLKALESSDLTEVVGYGFYLYKCQTKWMPQSMAE
ParentalWHRQRQERGMLKLAEAMNALELGPWMK
WH.Q.QERGMLKL.E.MNA..L.PW.K
RetrocopyWHCQCQERGMLKLVESMNAVKLRPWVK

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 0 .00 RPM
bodymap2_adrenal 0 .02 RPM 0 .00 RPM
bodymap2_brain 0 .02 RPM 0 .02 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .00 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .03 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .72 RPM
bodymap2_thyroid 0 .06 RPM 0 .04 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2067 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2067 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2067 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2067 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2067 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1489
Parental genes homology:
Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000026472 retrocopies
retro_cfam_1216, retro_cfam_524,
Choloepus hoffmanni ENSCHOG000000123381 retrocopy
retro_chof_2495,
Callithrix jacchus ENSCJAG000000099453 retrocopies
retro_cjac_1978, retro_cjac_62, retro_cjac_85,
Dasypus novemcinctus ENSDNOG000000115444 retrocopies
retro_dnov_115, retro_dnov_15, retro_dnov_2318, retro_dnov_53,
Dipodomys ordii ENSDORG000000003782 retrocopies
retro_dord_324, retro_dord_690,
Homo sapiens ENSG00000203909 1 retrocopy
retro_hsap_2067 ,
Gorilla gorilla ENSGGOG000000120011 retrocopy
retro_ggor_1489,
Myotis lucifugus ENSMLUG000000044631 retrocopy
retro_mluc_1051,
Macaca mulatta ENSMMUG000000004171 retrocopy
retro_mmul_1409,
Mus musculus ENSMUSG000000604617 retrocopies
retro_mmus_127, retro_mmus_1280, retro_mmus_1537, retro_mmus_1666, retro_mmus_2557, retro_mmus_3415, retro_mmus_58,
Pongo abelii ENSPPYG000000167711 retrocopy
retro_pabe_1680,
Pan troglodytes ENSPTRG000000295471 retrocopy
retro_ptro_1380,
Rattus norvegicus ENSRNOG000000001993 retrocopies
retro_rnor_106, retro_rnor_28, retro_rnor_76,
Sus scrofa ENSSSCG000000042832 retrocopies
retro_sscr_190, retro_sscr_487,
Ictidomys tridecemlineatus ENSSTOG000000053262 retrocopies
retro_itri_199, retro_itri_703,

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 = 0.03 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 .03 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 .03 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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