RetrogeneDB ID:

retro_hsap_3524

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:139659318..139660182(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000218565
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC7
Ensembl ID:ENSG00000168259
Aliases:DNAJC7, DJ11, DJC7, TPR2, TTC2
Description:DnaJ (Hsp40) homolog, subfamily C, member 7 [Source:HGNC Symbol;Acc:12392]


Retrocopy-Parental alignment summary:






>retro_hsap_3524
GAAGCACAGTCTTTGAAGCAACAAGGAAATGCACACTATGCCAAGGAAGATTACAACGAAGCTTATAACTATTAAACAAA
AGCCACAGATATGTGCCCTAAAAATGCTAGCTATCATAGTAATAGAGCAGCTACATTGATGATACTTGGAAGGTTCTGCG
AAGCCCATGGAGATACTTTCACAGTGAAATTGGATGATGGTTTCTTCTGGGGACATCTACGAGAGGGCAAGTGCCACCTC
TCTCCAGGGAATGCCATGGCAGCACATTGCAGTTTTCAGAGAGCCCTAGAACTGGATCATAACAATGCTCACTCACAACA
GGAGTTCACAAATGCTAATGCAGTCAAGGAATAGGAGAAAGTCATAGAAACAAGTTTTGAGAAGTGGGCTTTTCAGAAGG
TTGTTTTCTGCATGGACTATGCCCTAGAATTTGCCCCTGTCTGCCATCACTTCAATATCCCTCAAAGCAGAATGTTTAGC
AATGCTGGGTCGTTATCCAGAAGCACAGTCTGTGGCCAGTGACATTTTATGAACGGATTCCACCAATGTGGATGCTCTGT
ATGTACGCGGACCTTGCCTTTATTATGAAGATTGTACTGAGTAGGCAGTTGTTCAGTTTTTTGTACAGGCTCTCAGAGTG
GTTCCTGACCATGAGAAGGCCTGCCTTGCGTGCAGAAATGCCAGAGCACTTAACGCAAAGAAAGAAGACTGGAATAAAGC
GTTTAGGGAAGGAAATTACAAACTAGCTGATGAACTGTACGCAGAACCCCCGGGGTAGACCCCGACAACATAAAAGCAAT
TGCTAAACTCTACTGTAACCGGGATATGGTTAATTCCGAGCTTGGGAAACTAGATGATGCAATA

ORF - retro_hsap_3524 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.63 %
Parental protein coverage: 58.3 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDAQQSVRLDDSFV
EA...K.QGNA.YAK.DYNEAYNY.TKA.DMCPKNASY..NRAATLM.LGRF.EA.GD....V.LDD.F.
RetrocopyEAQSLKQQGNAHYAKEDYNEAYNY*TKATDMCPKNASYHSNRAATLMILGRFCEAHGDTF-TVKLDDGFF
ParentalRGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCMD
.GHLREGKCHLS.GNAMAA..SFQRALELDH.NA..QQEF.NANAV.E.EK..ET.FEK..F.KVVFCMD
RetrocopyWGHLREGKCHLSPGNAMAAHCSFQRALELDHNNAHSQQEFTNANAVKE*EKVIETSFEKWAFQKVVFCMD
ParentalRALEFAPACHRFKI-LKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKA-VQFFV
.ALEFAP.CH.F.I.LKAECLAMLGRYPEAQSVASDIL..DSTN.DALYVRG.CLYYEDC.E.A.VQFFV
RetrocopyYALEFAPVCHHFNI>LKAECLAMLGRYPEAQSVASDIL*TDSTNVDALYVRGPCLYYEDCTE*AVVQFFV
ParentalQALRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTE-ALGIDPNNIKTNAKLYCNRGTV
QALR..PDHEKAC.ACRNA.AL.AKKED.NKAF.EGNYKLA.ELY.E...G.DP.NIK..AKLYCNR..V
RetrocopyQALRVVPDHEKACLACRNARALNAKKEDWNKAFREGNYKLADELYAE<TPGVDPDNIKAIAKLYCNRDMV
ParentalNSKLRKLDDAI
NS.L.KLDDAI
RetrocopyNSELGKLDDAI

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 62 .64 RPM
bodymap2_adrenal 0 .00 RPM 72 .54 RPM
bodymap2_brain 0 .00 RPM 90 .46 RPM
bodymap2_breast 0 .00 RPM 46 .67 RPM
bodymap2_colon 0 .00 RPM 54 .72 RPM
bodymap2_heart 0 .00 RPM 46 .82 RPM
bodymap2_kidney 0 .00 RPM 75 .92 RPM
bodymap2_liver 0 .00 RPM 31 .98 RPM
bodymap2_lung 0 .00 RPM 43 .95 RPM
bodymap2_lymph_node 0 .09 RPM 62 .70 RPM
bodymap2_ovary 0 .00 RPM 78 .96 RPM
bodymap2_prostate 0 .00 RPM 57 .59 RPM
bodymap2_skeletal_muscle 0 .00 RPM 68 .77 RPM
bodymap2_testis 0 .00 RPM 77 .81 RPM
bodymap2_thyroid 0 .00 RPM 88 .83 RPM
bodymap2_white_blood_cells 0 .00 RPM 71 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3524 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3524 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1598871743 libraries61 libraries21 libraries3 libraries1 library

The graphical summary, for retro_hsap_3524 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3524 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3524 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2393
Gorilla gorilla retro_ggor_2382
Pongo abelii retro_pabe_2911
Macaca mulatta retro_mmul_1854
Parental genes homology:
Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000157491 retrocopy
retro_cfam_451,
Callithrix jacchus ENSCJAG000000356992 retrocopies
retro_cjac_2381, retro_cjac_2475,
Homo sapiens ENSG00000168259 1 retrocopy
retro_hsap_3524 ,
Gorilla gorilla ENSGGOG000000102302 retrocopies
retro_ggor_2382, retro_ggor_396,
Myotis lucifugus ENSMLUG000000119682 retrocopies
retro_mluc_1232, retro_mluc_1527,
Macaca mulatta ENSMMUG000000161183 retrocopies
retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys ENSNLEG000000112302 retrocopies
retro_nleu_1569, retro_nleu_490,
Pongo abelii ENSPPYG000000084022 retrocopies
retro_pabe_2911, retro_pabe_317,
Pan troglodytes ENSPTRG000000091882 retrocopies
retro_ptro_2393, retro_ptro_304,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 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 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 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 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .06 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 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 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 .02 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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