RetrogeneDB ID:

retro_hsap_54

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:128181389..128182088(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179407
Aliases:DNAJB8, CT156, DJ6
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJB6
Ensembl ID:ENSG00000105993
Aliases:DNAJB6, DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1
Description:DnaJ (Hsp40) homolog, subfamily B, member 6 [Source:HGNC Symbol;Acc:14888]


Retrocopy-Parental alignment summary:






>retro_hsap_54
ATGGCTAACTACTACGAAGTGCTGGGCGTGCAGGCCAGCGCTTCCCCGGAGGACATCAAGAAAGCCTACCGCAAGCTGGC
CCTTCGTTGGCACCCCGACAAGAACCCTGACAATAAGGAGGAGGCGGAGAAGAAGTTCAAGCTGGTGTCTGAGGCCTATG
AGGTTCTGTCTGACTCCAAGAAACGCTCCCTGTATGACCGTGCTGGCTGTGACAGCTGGCGGGCTGGTGGCGGGGCCAGC
ACGCCCTACCACAGCCCCTTCGACACCGGCTACACCTTCCGTAACCCTGAGGACATCTTCCGGGAGTTTTTTGGTGGCCT
GGACCCTTTCTCCTTTGAGTTCTGGGACAGCCCATTCAATAGTGACCGTGGTGGCCGGGGCCATGGCCTGAGGGGGGCCT
TCTCGGCAGGCTTTGGAGAATTTCCGGCCTTCATGGAGGCCTTCTCATCCTTCAACATGCTGGGCTGCAGCGGGGGCAGC
CACACCACCTTCTCATCCACCTCCTTCGGGGGCTCCAGTTCTGGCAGCTCGGGGTTCAAGTCGGTGATGTCGTCCACCGA
GATGATCAATGGCCACAAGGTCACCACCAAGCGCATCGTGGAGAACGGGCAGGAGCGCGTGGAGGTGGAGGAAGACGGGC
AGCTCAAGTCGGTGACTGTGAACGGCAAGGAGCAGCTCAAATGGATGGACAGCAAGTAG

ORF - retro_hsap_54 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.95 %
Parental protein coverage: 93.36 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVDYYEVLGVQRHASPEDIKKAYRKLALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGK
M..YYEVLGVQ..ASPEDIKKAYRKLAL.WHPDKNP.NKEEAE.KFK.V.EAYEVLSD.KKR..YD..G.
RetrocopyMANYYEVLGVQASASPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVLSDSKKRSLYDRAGC
ParentalEGLNGGGGGGSHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFFEDPFEDFFGNR-RGPRGSRSRGTGS
.....GGG......SPF..G.TFRNP.D.FREFFGG.DPFSF.F...PF....G.R..G.RG..S.G.G.
RetrocopyDSWRAGGGASTPYHSPFDTGYTFRNPEDIFREFFGGLDPFSFEFWDSPFNSDRGGRGHGLRGAFSAGFGE
ParentalF---FSAFSGFPSFG-SGFSSFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKMVNGRKITT
F.....AFS.F...G.SG.S......TSFG.....G...F.S.......M.N.....T.....NG.....
RetrocopyFPAFMEAFSSFNMLGCSGGSHTTFSSTSFGG-SSSGSSGFKSV-MSSTEMINGHKVTTKRIVENGQE--R
ParentalKRIVENGQ-ERVEVEEDGQLK
....E.GQ...V.V....QLK
RetrocopyVEVEEDGQLKSVTVNGKEQLK

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 .12 RPM 81 .30 RPM
bodymap2_adrenal 0 .08 RPM 80 .67 RPM
bodymap2_brain 0 .00 RPM 114 .06 RPM
bodymap2_breast 0 .00 RPM 99 .30 RPM
bodymap2_colon 0 .00 RPM 180 .15 RPM
bodymap2_heart 0 .00 RPM 132 .94 RPM
bodymap2_kidney 0 .00 RPM 90 .02 RPM
bodymap2_liver 0 .00 RPM 26 .47 RPM
bodymap2_lung 0 .00 RPM 117 .26 RPM
bodymap2_lymph_node 0 .00 RPM 182 .88 RPM
bodymap2_ovary 0 .00 RPM 78 .07 RPM
bodymap2_prostate 0 .00 RPM 151 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 278 .60 RPM
bodymap2_testis 21 .45 RPM 194 .62 RPM
bodymap2_thyroid 0 .00 RPM 122 .59 RPM
bodymap2_white_blood_cells 0 .00 RPM 92 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_54 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_54 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_1287431820 libraries5 libraries1 library0 libraries3 libraries
TSS #2 TSS_1287441826 libraries0 libraries2 libraries1 library0 libraries

The graphical summary, for retro_hsap_54 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_54 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_54 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_201
Callithrix jacchus retro_cjac_104
Parental genes homology:
Parental genes homology involve 27 parental genes, and 122 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013323 retrocopies
retro_amel_127, retro_amel_685, retro_amel_95,
Bos taurus ENSBTAG000000007713 retrocopies
retro_btau_163, retro_btau_222, retro_btau_248,
Canis familiaris ENSCAFG000000051746 retrocopies
retro_cfam_155, retro_cfam_201, retro_cfam_2085, retro_cfam_2131, retro_cfam_527, retro_cfam_8,
Callithrix jacchus ENSCJAG000000052887 retrocopies
retro_cjac_104, retro_cjac_1455, retro_cjac_1648, retro_cjac_1692, retro_cjac_2922, retro_cjac_3880, retro_cjac_948,
Cavia porcellus ENSCPOG0000001395317 retrocopies
retro_cpor_1035, retro_cpor_1074, retro_cpor_1147, retro_cpor_1352, retro_cpor_1360, retro_cpor_1364, retro_cpor_259, retro_cpor_325, retro_cpor_38, retro_cpor_40, retro_cpor_538, retro_cpor_610, retro_cpor_720, retro_cpor_793, retro_cpor_814, retro_cpor_840, retro_cpor_952,
Equus caballus ENSECAG000000090052 retrocopies
retro_ecab_105, retro_ecab_22,
Felis catus ENSFCAG000000156542 retrocopies
retro_fcat_1072, retro_fcat_91,
Homo sapiens ENSG000001011521 retrocopy
retro_hsap_4028,
Homo sapiens ENSG00000105993 9 retrocopies
retro_hsap_103, retro_hsap_166, retro_hsap_2399, retro_hsap_2400, retro_hsap_4031, retro_hsap_519, retro_hsap_54 , retro_hsap_889, retro_hsap_939,
Gorilla gorilla ENSGGOG000000047036 retrocopies
retro_ggor_1819, retro_ggor_201, retro_ggor_210, retro_ggor_251, retro_ggor_478, retro_ggor_719,
Loxodonta africana ENSLAFG000000133844 retrocopies
retro_lafr_105, retro_lafr_107, retro_lafr_260, retro_lafr_468,
Microcebus murinus ENSMICG000000097601 retrocopy
retro_mmur_474,
Myotis lucifugus ENSMLUG000000091234 retrocopies
retro_mluc_1371, retro_mluc_147, retro_mluc_304, retro_mluc_333,
Macaca mulatta ENSMMUG000000031766 retrocopies
retro_mmul_1050, retro_mmul_165, retro_mmul_2326, retro_mmul_243, retro_mmul_379, retro_mmul_970,
Mustela putorius furoENSMPUG000000097974 retrocopies
retro_mputfur_1084, retro_mputfur_11, retro_mputfur_1199, retro_mputfur_70,
Mus musculus ENSMUSG000000291316 retrocopies
retro_mmus_113, retro_mmus_171, retro_mmus_2023, retro_mmus_3273, retro_mmus_435, retro_mmus_870,
Nomascus leucogenys ENSNLEG000000013805 retrocopies
retro_nleu_1524, retro_nleu_2, retro_nleu_2063, retro_nleu_2820, retro_nleu_52,
Oryctolagus cuniculus ENSOCUG000000000642 retrocopies
retro_ocun_240, retro_ocun_83,
Otolemur garnettii ENSOGAG000000106402 retrocopies
retro_ogar_248, retro_ogar_3412,
Pongo abelii ENSPPYG000000182284 retrocopies
retro_pabe_100, retro_pabe_2165, retro_pabe_226, retro_pabe_669,
Pelodiscus sinensis ENSPSIG000000181021 retrocopy
retro_psin_19,
Pteropus vampyrus ENSPVAG000000001551 retrocopy
retro_pvam_24,
Rattus norvegicus ENSRNOG000000103536 retrocopies
retro_rnor_1680, retro_rnor_1930, retro_rnor_212, retro_rnor_2673, retro_rnor_60, retro_rnor_641,
Ictidomys tridecemlineatus ENSSTOG000000029647 retrocopies
retro_itri_1090, retro_itri_1143, retro_itri_169, retro_itri_54, retro_itri_74, retro_itri_832, retro_itri_85,
Tupaia belangeri ENSTBEG000000095867 retrocopies
retro_tbel_1521, retro_tbel_1533, retro_tbel_1571, retro_tbel_1978, retro_tbel_3918, retro_tbel_4142, retro_tbel_67,
Tarsius syrichta ENSTSYG000000054484 retrocopies
retro_tsyr_1358, retro_tsyr_297, retro_tsyr_360, retro_tsyr_491,
Tursiops truncatus ENSTTRG000000139292 retrocopies
retro_ttru_1864, retro_ttru_637,

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 = 0.02 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 .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 .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 .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).



Copyright © RetrogeneDB 2014-2017