RetrogeneDB ID:

retro_hsap_1545

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:32057951..32059320(-)
Located in intron of:ENSG00000169918
Retrocopy
information
Ensembl ID:ENSG00000259358
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DEPDC1
Ensembl ID:ENSG00000024526
Aliases:DEPDC1, DEP.8, DEPDC1-V2, DEPDC1A, SDP35
Description:DEP domain containing 1 [Source:HGNC Symbol;Acc:22949]


Retrocopy-Parental alignment summary:






>retro_hsap_1545
AAAGAAGAATCAGATTCTACTGAGAGACTACAGATAAGCAATCCAGGATTTCAAGAAAGATGTGCTAAGAAAATGCAGCT
AGTTAATTTAAGAAACAGAAGAGTGAGTGCTAATGACATAATGGGAGGAAGTTGTCATAATTTAATAGGGTTAAGTAGTA
TGCGTGATCTATCCTCTAACAGCAAACCAAGGTGCTATTCTTTGGAAGGAATTGTAGATGTGTCAGGGAATTCAAGTAAA
GAGGCATCCAGTGTCTTCCATCAATCTTTTCCGAACATAGAAGGACAAAATAATAAACTGTTTTTAGAGTCTAAGCCCAA
ACAGGAATTCCTGTTGAATCTTCATTCAGAGGAAAATATTCAAAAGCCATTCAGTGCTGGTTTTAAGAGAACCTCTACTT
TGATTGTTCAAGACCAAGAGGAGTTGTGTAATGGGAAATGCAAGTCAGAACAGCTTTGAAGGTCTCAGAGTTTGCTTTTA
ACAAGTAGTACAAGAAGGAATAGTTATTATCAATACACCAGTGGCTGAAATTACCATGAAACCAAATGTTGGACAAGGCA
GCACAAGTGTGCAAACAGCTATGGAAAGTGAACTTGGAGAGTCTAGTGCCACAATCAATAAAAGACTCTGCAAAAGTACA
ATAGAACTTTCAGAAGACTCTTTACTTCCAGCTTCTTCTGTGTTGACTGGCACACAAAGTTTGCTGCAACCTCATTTAGA
GAGGGTTGCCATCGATGCTCTACAGTTATGTTGTTTGTTATTTCCCCCACCAAATCATAGAAAGCTTCAACTTTTAATGC
GTATGATTTCCCGAATGAGTCAAAATGTTGATATGCCCAAACTTCATGATGCAATGGGTGCGAGATCACTGTTGATACAT
ACCGTTTCTCAATGTGTGTTATGCTGTGCTGAAGAAGTGGACCTTGATGAGCTTCTTGCTGGAAGATTAGTTTCTTTCTT
AATGGATCATGATCAGGAAATTCTTCAAGTACCCTCTTACTTGCAGACTGCAGTGGAAAAACATCTTGACTACTTAAAAA
GGGGACATATTGAAAGTCCTGGAGATGGACTATTTGCTCCTTTGCCAACTTACTCATACGGTAAGCAGATTAGTGCTCAG
GAGTTTGATGAGCAAAAAATTTCTACCTCTCAAGCTGCAATTGCAGAACTTTTAGAAAATATTGTTAAAAACAGGACTTT
ACCTCTAAAGGAGAAAAGAAAAAAACTAAAATAGTTTCAGAAGGAATATCCTTTGATATATCAGAAAAGATTTCCAACCA
TGGAGAGTGAAGCAGCACTTTTTGGTGACAAACCTACAATCAAGCAACCAATGCTGATTTTAAGAAAACCAAAGTTCTGT
AGTCTAAGA

ORF - retro_hsap_1545 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.56 %
Parental protein coverage: 56.23 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalKEESDSTERLQISNPGFQERCAKKMQLVNLRNRRVSANDIMGGSCHNLIGLSNMHDLSSNSKPRCCSLEG
KEESDSTERLQISNPGFQERCAKKMQLVNLRNRRVSANDIMGGSCHNLIGLS.M.DLSSNSKPRC.SLEG
RetrocopyKEESDSTERLQISNPGFQERCAKKMQLVNLRNRRVSANDIMGGSCHNLIGLSSMRDLSSNSKPRCYSLEG
ParentalIVDVPGNSSKEASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTLTVQDQE
IVDV.GNSSKEASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTL.VQDQE
RetrocopyIVDVSGNSSKEASSVFHQSFPNIEGQNNKLFLESKPKQEFLLNLHSEENIQKPFSAGFKRTSTLIVQDQE
ParentalELCNGKCKSKQLCRSQSLLLRSSTRRNSY-INTPVAEIIMKPNVGQGSTSVQTAMESELGESSATINKRL
ELCNGKCKS.QL.RSQSLLL.SSTRRNSY.INTPVAEI.MKPNVGQGSTSVQTAMESELGESSATINKRL
RetrocopyELCNGKCKSEQL*RSQSLLLTSSTRRNSY>INTPVAEITMKPNVGQGSTSVQTAMESELGESSATINKRL
ParentalCKSTIELSENSLLPASSMLTGTQSLLQPHLERVAIDALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMP
CKSTIELSE.SLLPASS.LTGTQSLLQPHLERVAIDALQLCCLL.PPPN.RKLQLLMRMISRMSQNVDMP
RetrocopyCKSTIELSEDSLLPASSVLTGTQSLLQPHLERVAIDALQLCCLLFPPPNHRKLQLLMRMISRMSQNVDMP
ParentalKLHDAMGTRSLMIHTFSRCVLCCAEEVDLDELLAGRLVSFLMDHHQEILQVPSYLQTAVEKHLDYLKKGH
KLHDAMG.RSL.IHT.S.CVLCCAEEVDLDELLAGRLVSFLMDH.QEILQVPSYLQTAVEKHLDYLK.GH
RetrocopyKLHDAMGARSLLIHTVSQCVLCCAEEVDLDELLAGRLVSFLMDHDQEILQVPSYLQTAVEKHLDYLKRGH
ParentalIENPGDGLFAPLPTYSYCKQISAQEFDEQKVSTSQAAIAELLENIIKNRSLPLKEKRKKLKQFQKEYPLI
IE.PGDGLFAPLPTYSY.KQISAQEFDEQK.STSQAAIAELLENI.KNR.LPLKE.......FQKEYPLI
RetrocopyIESPGDGLFAPLPTYSYGKQISAQEFDEQKISTSQAAIAELLENIVKNRTLPLKEXXXXXX*FQKEYPLI
ParentalYQKRFPTTESEAALFGDKPTIKQPMLILRKPKFRSLR
YQKRFPT.ESEAALFGDKPTIKQPMLILRKPKF.SLR
RetrocopyYQKRFPTMESEAALFGDKPTIKQPMLILRKPKFCSLR

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 .08 RPM 0 .54 RPM
bodymap2_adrenal 0 .00 RPM 0 .20 RPM
bodymap2_brain 0 .00 RPM 0 .61 RPM
bodymap2_breast 0 .00 RPM 0 .99 RPM
bodymap2_colon 0 .00 RPM 1 .18 RPM
bodymap2_heart 0 .02 RPM 0 .70 RPM
bodymap2_kidney 0 .00 RPM 0 .72 RPM
bodymap2_liver 0 .00 RPM 0 .04 RPM
bodymap2_lung 0 .00 RPM 0 .91 RPM
bodymap2_lymph_node 0 .00 RPM 1 .44 RPM
bodymap2_ovary 0 .00 RPM 0 .39 RPM
bodymap2_prostate 0 .00 RPM 0 .48 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 25 .45 RPM
bodymap2_thyroid 0 .00 RPM 0 .40 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_1545 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1545 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1545 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1545 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1545 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1041
Gorilla gorilla retro_ggor_1176
Parental genes homology:
Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000138391 retrocopy
retro_cpor_735,
Homo sapiens ENSG00000024526 2 retrocopies
retro_hsap_1545 , retro_hsap_4206,
Gorilla gorilla ENSGGOG000000163161 retrocopy
retro_ggor_1176,
Macaca mulatta ENSMMUG000000177661 retrocopy
retro_mmul_1176,
Mus musculus ENSMUSG000000281751 retrocopy
retro_mmus_3028,
Nomascus leucogenys ENSNLEG000000093341 retrocopy
retro_nleu_2931,
Otolemur garnettii ENSOGAG000000009341 retrocopy
retro_ogar_1907,
Pongo abelii ENSPPYG000000012481 retrocopy
retro_pabe_3441,
Pan troglodytes ENSPTRG000000008472 retrocopies
retro_ptro_1041, retro_ptro_2855,

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 = 0.05 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 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 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 .05 RPM
TSI_NA20756 0 .03 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 .03 RPM
YRI_NA19114 0 .03 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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