RetrogeneDB ID:

retro_hsap_2648

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:51469995..51470470(+)
Located in intron of:ENSG00000145041
Retrocopy
information
Ensembl ID:ENSG00000270692
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DPPA3
Ensembl ID:ENSG00000187569
Aliases:DPPA3, STELLA
Description:developmental pluripotency associated 3 [Source:HGNC Symbol;Acc:19199]


Retrocopy-Parental alignment summary:






>retro_hsap_2648
ACAAAGTTTGATCCGACCTTGGTCCCAGAGTCTTCATAAATGCTCACTGAAGAAAATTCCCAGGATGATTCGGGGGCCTC
TCAAAACTTCTGCTTCAAGACGTTGATAAAGAACCTTAGTAACTTGACTATACACCCCAGTACTGAATTCCCTTCCCATC
TACCAGAAAATTCACCCCAACAACAATATACAGGAGCAATGATGCTCAGGGAAATCAGAGATGACTTGCTCTACATGAGA
GGGGTAAGAACACTGCTGTTTGCATAGAAAGAAAAGGATGGCAAAATTGAGATACATGTTACTCAGCAGAGTTCCTAGGC
TTGAAAGAGAACTAACAAACACTGGGCTTAAGAGAGTTCAGAATGAATCAAGTAGTGGACCATTCAGATGTTGCTGCAGT
TTCTGCATGTATAACCAATGGGATCCTTCTGAGGATGCTAGAATACGGAATTATGACACTGAGCCATGTCAGCCA

ORF - retro_hsap_2648 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.5 %
Parental protein coverage: 98.11 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSQFNPTYIPGSPQMLTEENSRDDSGASQ-ISSETLIKNLSNLTINASSESVSPLSEALLRRESVGAAVLR
..F.PT..P.S..MLTEENS.DDSGASQ.....TLIKNLSNLTI..S.E..S.L.E........GA..LR
RetrocopyTKFDPTLVPESS*MLTEENSQDDSGASQNFCFKTLIKNLSNLTIHPSTEFPSHLPENSPQQQYTGAMMLR
ParentalEIEDEWLYSRRGVRTLLSVQREK-MARLRYMLLGGVRTHERRPTNKEPKGVKKESR--PFKCPCSFCVSN
EI.D..LY.R.GVRTLL....EK.MA.LRYMLL..V...ER..TN...K.V..ES...PF.C.CSFC..N
RetrocopyEIRDDLLYMR-GVRTLLFA*KEK>MAKLRYMLLSRVPRLERELTNTGLKRVQNESSSGPFRCCCSFCMYN
ParentalGWDPSENARIGNQDTKPLQP
.WDPSE.ARI.N.DT.P.QP
RetrocopyQWDPSEDARIRNYDTEPCQP

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 .22 RPM 0 .00 RPM
bodymap2_adrenal 0 .20 RPM 0 .00 RPM
bodymap2_brain 0 .02 RPM 0 .00 RPM
bodymap2_breast 0 .21 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .02 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 .02 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .04 RPM 0 .47 RPM
bodymap2_thyroid 0 .08 RPM 0 .00 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_2648 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2648 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2648 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2648 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2648 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1783
Gorilla gorilla retro_ggor_1849
Pongo abelii retro_pabe_2323
Callithrix jacchus retro_cjac_1329
Parental genes homology:
Parental genes homology involve 13 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000466091 retrocopy
retro_btau_1001,
Canis familiaris ENSCAFG000000320921 retrocopy
retro_cfam_1926,
Callithrix jacchus ENSCJAG0000000540910 retrocopies
retro_cjac_1329, retro_cjac_1446, retro_cjac_1465, retro_cjac_1474, retro_cjac_2052, retro_cjac_2628, retro_cjac_3162, retro_cjac_4006, retro_cjac_622, retro_cjac_730,
Homo sapiens ENSG00000187569 6 retrocopies
retro_hsap_1043, retro_hsap_1323, retro_hsap_1618, retro_hsap_2648 , retro_hsap_4010, retro_hsap_4887,
Gorilla gorilla ENSGGOG000000130404 retrocopies
retro_ggor_1849, retro_ggor_2693, retro_ggor_3052, retro_ggor_823,
Mustela putorius furoENSMPUG000000175303 retrocopies
retro_mputfur_1220, retro_mputfur_1452, retro_mputfur_520,
Mus musculus ENSMUSG000000463234 retrocopies
retro_mmus_1186, retro_mmus_1682, retro_mmus_1838, retro_mmus_3598,
Nomascus leucogenys ENSNLEG000000268872 retrocopies
retro_nleu_2041, retro_nleu_914,
Otolemur garnettii ENSOGAG000000248137 retrocopies
retro_ogar_1514, retro_ogar_1618, retro_ogar_1775, retro_ogar_1780, retro_ogar_1964, retro_ogar_2538, retro_ogar_3406,
Pongo abelii ENSPPYG000000042306 retrocopies
retro_pabe_1338, retro_pabe_1962, retro_pabe_2323, retro_pabe_3586, retro_pabe_873, retro_pabe_975,
Pan troglodytes ENSPTRG000000046177 retrocopies
retro_ptro_1085, retro_ptro_1783, retro_ptro_2701, retro_ptro_2722, retro_ptro_3148, retro_ptro_711, retro_ptro_904,
Rattus norvegicus ENSRNOG000000229504 retrocopies
retro_rnor_1249, retro_rnor_1816, retro_rnor_2234, retro_rnor_395,
Tursiops truncatus ENSTTRG000000007513 retrocopies
retro_ttru_1293, retro_ttru_1911, retro_ttru_84,

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 = 0.14 RPM Legend:


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