RetrogeneDB ID:

retro_hsap_4312

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:128134603..128134971(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227845
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC15
Ensembl ID:ENSG00000120675
Aliases:DNAJC15, DNAJD1, HSD18, MCJ
Description:DnaJ (Hsp40) homolog, subfamily C, member 15 [Source:HGNC Symbol;Acc:20325]


Retrocopy-Parental alignment summary:






>retro_hsap_4312
GACGCAGATACCAACCAGCAGGGACTGGCAAGAACTGTGACAGCTGCAGGGCTGGGTGCTGCTGCTCTTGCCTTTGCAGG
TCGCTGTGCGTCGCAGTCCTGGAAACCTCTAGAACAAGGATCACAGAAGCAGTAGAGAACCTTTGAACTCCTAGCCTGTC
ATCCTATTACAAAGGAGGATTTGAACAGAAAATGAGTAGGAGAAAAGCTAGTGTTATTTTAGGTGTAAGTTCACCTGCTG
GCAAGGCTAAGATTAGAGCAGCTCACAGGAGAATCGTGATTTTGAATCACCCAGATAAAGGTGGATCTCCCTACTTAGCA
ACCAAAATAAATGAAACAGAAGATTTGCGAGAAGCGACCACCGATCAC

ORF - retro_hsap_4312 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.16 %
Parental protein coverage: 82.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalDADVDQQRLVRSLIAVGLGVAALAFAGRYAFRIWKPLEQV-ITETAKKISTPSFSSYYKGGFEQKMSRRE
DAD..QQ.L.R...A.GLG.AALAFAGR.A...WKPLEQ..ITE......TPS.SSYYKGGFEQKMSRR.
RetrocopyDADTNQQGLARTVTAAGLGAAALAFAGRCASQSWKPLEQG<ITEAVENL*TPSLSSYYKGGFEQKMSRRK
ParentalAGLILGVSPSAGKAKIRTAHRRVMILNHPDKGGSPYVAAKINEAKDLLETTTKH
A..ILGVS..AGKAKIR.AHRR..ILNHPDKGGSPY.A.KINE..DL.E.TT.H
RetrocopyASVILGVSSPAGKAKIRAAHRRIVILNHPDKGGSPYLATKINETEDLREATTDH

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 25 .98 RPM
bodymap2_adrenal 0 .00 RPM 35 .21 RPM
bodymap2_brain 0 .00 RPM 33 .57 RPM
bodymap2_breast 0 .00 RPM 43 .50 RPM
bodymap2_colon 0 .00 RPM 38 .88 RPM
bodymap2_heart 0 .00 RPM 48 .05 RPM
bodymap2_kidney 0 .00 RPM 65 .80 RPM
bodymap2_liver 0 .00 RPM 35 .45 RPM
bodymap2_lung 0 .00 RPM 20 .25 RPM
bodymap2_lymph_node 0 .00 RPM 33 .26 RPM
bodymap2_ovary 0 .00 RPM 21 .73 RPM
bodymap2_prostate 0 .00 RPM 26 .66 RPM
bodymap2_skeletal_muscle 0 .00 RPM 23 .59 RPM
bodymap2_testis 0 .06 RPM 49 .75 RPM
bodymap2_thyroid 0 .00 RPM 35 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 38 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4312 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4312 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4312 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4312 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4312 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2920
Gorilla gorilla retro_ggor_2882
Pongo abelii retro_pabe_3508
Macaca mulatta retro_mmul_1169
Callithrix jacchus retro_cjac_634
Parental genes homology:
Parental genes homology involve 25 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000347851 retrocopy
retro_btau_1624,
Canis familiaris ENSCAFG000000046641 retrocopy
retro_cfam_939,
Callithrix jacchus ENSCJAG000000175892 retrocopies
retro_cjac_1663, retro_cjac_634,
Cavia porcellus ENSCPOG000000034851 retrocopy
retro_cpor_327,
Equus caballus ENSECAG000000077571 retrocopy
retro_ecab_561,
Erinaceus europaeus ENSEEUG000000087855 retrocopies
retro_eeur_360, retro_eeur_608, retro_eeur_64, retro_eeur_93, retro_eeur_95,
Felis catus ENSFCAG000000226321 retrocopy
retro_fcat_259,
Homo sapiens ENSG00000120675 2 retrocopies
retro_hsap_3331, retro_hsap_4312 ,
Homo sapiens ENSG000002059818 retrocopies
retro_hsap_1330, retro_hsap_2061, retro_hsap_2062, retro_hsap_2349, retro_hsap_3497, retro_hsap_387, retro_hsap_538, retro_hsap_583,
Gorilla gorilla ENSGGOG000000163382 retrocopies
retro_ggor_1294, retro_ggor_2882,
Loxodonta africana ENSLAFG000000043432 retrocopies
retro_lafr_287, retro_lafr_942,
Myotis lucifugus ENSMLUG000000086843 retrocopies
retro_mluc_1358, retro_mluc_1544, retro_mluc_520,
Macaca mulatta ENSMMUG000000136891 retrocopy
retro_mmul_1169,
Mustela putorius furoENSMPUG000000017041 retrocopy
retro_mputfur_1065,
Nomascus leucogenys ENSNLEG000000017594 retrocopies
retro_nleu_1408, retro_nleu_1464, retro_nleu_1675, retro_nleu_585,
Oryctolagus cuniculus ENSOCUG000000016964 retrocopies
retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936,
Ochotona princeps ENSOPRG000000161915 retrocopies
retro_opri_1038, retro_opri_235, retro_opri_285, retro_opri_756, retro_opri_766,
Pongo abelii ENSPPYG000000053231 retrocopy
retro_pabe_3508,
Pan troglodytes ENSPTRG000000058312 retrocopies
retro_ptro_2148, retro_ptro_2920,
Pteropus vampyrus ENSPVAG000000112811 retrocopy
retro_pvam_807,
Sorex araneus ENSSARG000000076831 retrocopy
retro_sara_658,
Ictidomys tridecemlineatus ENSSTOG000000128051 retrocopy
retro_itri_1710,
Taeniopygia guttata ENSTGUG000000123642 retrocopies
retro_tgut_20, retro_tgut_45,
Tursiops truncatus ENSTTRG000000155801 retrocopy
retro_ttru_1021,
Vicugna pacos ENSVPAG000000014451 retrocopy
retro_vpac_113,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 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 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 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 .02 RPM
YRI_NA19223 0 .06 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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