RetrogeneDB ID:

retro_hsap_4119

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:143049454..143049928(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254183
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC8
Ensembl ID:ENSG00000126698
Aliases:DNAJC8, HSPC331, SPF31
Description:DnaJ (Hsp40) homolog, subfamily C, member 8 [Source:HGNC Symbol;Acc:15470]


Retrocopy-Parental alignment summary:






>retro_hsap_4119
GCACAAACAGCTTTTGAAGCTGTGGACAAAGCTTGCAAGTTGCTACTGGATCAGGAGCAAAAGAAGAAGGTCCTGGATGT
AATTCAGGCAGGAAAGGAATACGTGGAACGCAGTGTGAAAGAGTGAAAAAAACAATTAAAGAAGGAAGGAGAACCTACGA
GTTTAGCAGAGGCTGATTCTGAGCTGTTCAAACAAGCTGTATGTATACAGACAATGAAACGCTTTGCTGAGCAGGAAATT
AAAAGGAAAGAGAAAGAAGCCAAAGAGATGCATGAAAGGAAACGACAAAGGGAAGAAGACACTGAAGCTCAAGAAAAAGC
CAAATGAGAAAGAAAGCGGCAGAAAAACTTTGAAGAAAGTCGTGATGGTCATGTGGACAGCTGGCGAAACTTCCAAGCCA
ATACAAAGGGGAAGAAAGAGAATAAAAACCAGACCTTCCTGAGACAACCAAAAGTAAAAATGGAGCCGTGTGAA

ORF - retro_hsap_4119 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.65 %
Parental protein coverage: 62.45 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAQKAFEAVDKAYKLLLDQEQKKRALDVIQAGKEYVEHTVKERKKQLKKEGKPTIVEEDDPELFKQAVYKQ
AQ.AFEAVDKA.KLLLDQEQKK..LDVIQAGKEYVE..VKE.KKQLKKEG.PT...E.D.ELFKQAV..Q
RetrocopyAQTAFEAVDKACKLLLDQEQKKKVLDVIQAGKEYVERSVKE*KKQLKKEGEPTSLAEADSELFKQAVCIQ
ParentalTMKLFAELEIKRKEREAKEMHERKRQREEEIEAQEKAKREREWQKNFEESRDGRVDSWRNFQANTKGKKE
TMK.FAE.EIKRKE.EAKEMHERKRQREE..EAQEKAK.ER..QKNFEESRDG.VDSWRNFQANTKGKKE
RetrocopyTMKRFAEQEIKRKEKEAKEMHERKRQREEDTEAQEKAK*ERKRQKNFEESRDGHVDSWRNFQANTKGKKE
ParentalKKNRTFLRPPKVKMEQRE
.KN.TFLR.PKVKME..E
RetrocopyNKNQTFLRQPKVKMEPCE

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 63 .01 RPM
bodymap2_adrenal 0 .00 RPM 95 .59 RPM
bodymap2_brain 0 .00 RPM 89 .96 RPM
bodymap2_breast 0 .00 RPM 63 .99 RPM
bodymap2_colon 0 .00 RPM 99 .21 RPM
bodymap2_heart 0 .00 RPM 39 .71 RPM
bodymap2_kidney 0 .00 RPM 73 .89 RPM
bodymap2_liver 0 .00 RPM 34 .68 RPM
bodymap2_lung 0 .00 RPM 65 .98 RPM
bodymap2_lymph_node 0 .00 RPM 68 .38 RPM
bodymap2_ovary 0 .00 RPM 98 .58 RPM
bodymap2_prostate 0 .00 RPM 90 .53 RPM
bodymap2_skeletal_muscle 0 .00 RPM 34 .85 RPM
bodymap2_testis 0 .00 RPM 91 .25 RPM
bodymap2_thyroid 0 .00 RPM 106 .47 RPM
bodymap2_white_blood_cells 0 .00 RPM 100 .23 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4119 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4119 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4119 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4119 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4119 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000112311 retrocopy
retro_amel_703,
Bos taurus ENSBTAG000000183852 retrocopies
retro_btau_1332, retro_btau_794,
Canis familiaris ENSCAFG000000118852 retrocopies
retro_cfam_1506, retro_cfam_1663,
Choloepus hoffmanni ENSCHOG000000096491 retrocopy
retro_chof_1545,
Dasypus novemcinctus ENSDNOG000000154522 retrocopies
retro_dnov_133, retro_dnov_914,
Erinaceus europaeus ENSEEUG000000111362 retrocopies
retro_eeur_536, retro_eeur_638,
Echinops telfairi ENSETEG000000083484 retrocopies
retro_etel_374, retro_etel_502, retro_etel_745, retro_etel_846,
Felis catus ENSFCAG000000133931 retrocopy
retro_fcat_203,
Homo sapiens ENSG00000126698 3 retrocopies
retro_hsap_1319, retro_hsap_2840, retro_hsap_4119 ,
Gorilla gorilla ENSGGOG000000008212 retrocopies
retro_ggor_1030, retro_ggor_2766,
Microcebus murinus ENSMICG000000012225 retrocopies
retro_mmur_1152, retro_mmur_1355, retro_mmur_343, retro_mmur_601, retro_mmur_935,
Macaca mulatta ENSMMUG000000170804 retrocopies
retro_mmul_2004, retro_mmul_2078, retro_mmul_2168, retro_mmul_228,
Mustela putorius furoENSMPUG000000155401 retrocopy
retro_mputfur_202,
Mus musculus ENSMUSG000000544051 retrocopy
retro_mmus_916,
Nomascus leucogenys ENSNLEG000000097623 retrocopies
retro_nleu_1401, retro_nleu_1594, retro_nleu_2701,
Otolemur garnettii ENSOGAG000000155974 retrocopies
retro_ogar_2422, retro_ogar_2595, retro_ogar_3219, retro_ogar_84,
Pongo abelii ENSPPYG000000258332 retrocopies
retro_pabe_2351, retro_pabe_3382,
Pelodiscus sinensis ENSPSIG000000177211 retrocopy
retro_psin_34,
Pteropus vampyrus ENSPVAG000000176191 retrocopy
retro_pvam_1057,
Rattus norvegicus ENSRNOG000000132551 retrocopy
retro_rnor_488,
Ictidomys tridecemlineatus ENSSTOG000000128342 retrocopies
retro_itri_1361, retro_itri_1775,
Tarsius syrichta ENSTSYG000000070573 retrocopies
retro_tsyr_137, retro_tsyr_1389, retro_tsyr_885,
Tursiops truncatus ENSTTRG000000000471 retrocopy
retro_ttru_1430,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 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 .04 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 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 .05 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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