RetrogeneDB ID:

retro_hsap_2349

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:178093980..178094192(-)
Located in intron of:ENSG00000116044
Retrocopy
information
Ensembl ID:ENSG00000225808
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC19
Ensembl ID:ENSG00000205981
Aliases:DNAJC19, PAM18, TIM14, TIMM14
Description:DnaJ (Hsp40) homolog, subfamily C, member 19 [Source:HGNC Symbol;Acc:30528]


Retrocopy-Parental alignment summary:






>retro_hsap_2349
GTTTTGCAAGTCAGGAAGCACATATAGCCTGAAGTAAAACAGGATTTTCAAAGTCTACCAAAATCTGCCTTCAGCGGTGG
CTATTAGAGAGGTGGGCTTGAACTAAAAAGGACAAAATGGGAAGCAGCAATACTACCTCTAAGCCTTACTGCCATTAAAG
GAAAAATAAGAGATGCTCAGTAACAAATATGATCTTAAATCGCCCAAAGAAG

ORF - retro_hsap_2349 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.49 %
Parental protein coverage: 62.07 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalVLQAMKHMEPQVKQVFQSLPKSAFSGGYYRGGFEPKMTKREAALILGVSPTANKGKIRDAHRRI-MLLNH
VLQ..KH..P.VKQ.FQSLPKSAFSGGY.RGG.E.K.TK.EAA.IL..S.TA.KGKIRDA...I.M.LN.
RetrocopyVLQVRKHI*PEVKQDFQSLPKSAFSGGY*RGGLELKRTKWEAA-ILPLSLTAIKGKIRDAQ*QI<MILNR
ParentalPDK
P.K
RetrocopyPKK

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 .83 RPM 16 .90 RPM
bodymap2_adrenal 2 .58 RPM 17 .83 RPM
bodymap2_brain 1 .10 RPM 28 .81 RPM
bodymap2_breast 0 .64 RPM 21 .23 RPM
bodymap2_colon 0 .12 RPM 28 .29 RPM
bodymap2_heart 0 .04 RPM 36 .05 RPM
bodymap2_kidney 1 .05 RPM 50 .56 RPM
bodymap2_liver 0 .06 RPM 17 .58 RPM
bodymap2_lung 2 .32 RPM 13 .01 RPM
bodymap2_lymph_node 0 .48 RPM 20 .08 RPM
bodymap2_ovary 1 .14 RPM 23 .92 RPM
bodymap2_prostate 0 .59 RPM 34 .12 RPM
bodymap2_skeletal_muscle 0 .29 RPM 15 .66 RPM
bodymap2_testis 0 .41 RPM 20 .30 RPM
bodymap2_thyroid 1 .05 RPM 31 .67 RPM
bodymap2_white_blood_cells 0 .10 RPM 14 .79 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_hsap_2349 in 8 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CGN POLR2A 2:178094279..178094743
ENCFF002CIH POLR2A 2:178094330..178094627
ENCFF002CJZ POLR2A 2:178094285..178094608
ENCFF002CKX POLR2A 2:178094332..178094445
ENCFF002CXR POLR2A 2:178094195..178094631
ENCFF002DBQ POLR2A 2:178094268..178094638
ENCFF002CHO POLR2A 2:178094058..178094821
ENCFF002DAY POLR2A 2:178093609..178094245

EST - click to see more details

No EST(s) were mapped for retro_hsap_2349 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2349 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2349 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2349 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1719
Gorilla gorilla retro_ggor_1783
Pongo abelii retro_pabe_2126
Macaca mulatta retro_mmul_946
Parental genes homology:
Parental genes homology involve 19 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000235131 retrocopy
retro_btau_127,
Canis familiaris ENSCAFG000000327148 retrocopies
retro_cfam_1256, retro_cfam_1306, retro_cfam_1451, retro_cfam_2015, retro_cfam_346, retro_cfam_389, retro_cfam_741, retro_cfam_819,
Callithrix jacchus ENSCJAG0000001279510 retrocopies
retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Dasypus novemcinctus ENSDNOG000000190671 retrocopy
retro_dnov_49,
Dipodomys ordii ENSDORG000000058627 retrocopies
retro_dord_232, retro_dord_295, retro_dord_320, retro_dord_53, retro_dord_586, retro_dord_684, retro_dord_794,
Erinaceus europaeus ENSEEUG000000069559 retrocopies
retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi ENSETEG000000068977 retrocopies
retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis ENSFALG000000082961 retrocopy
retro_falb_28,
Homo sapiens ENSG000001206752 retrocopies
retro_hsap_3331, retro_hsap_4312,
Homo sapiens ENSG00000205981 8 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,
Gallus gallus ENSGALG000000088521 retrocopy
retro_ggal_17,
Loxodonta africana ENSLAFG000000019105 retrocopies
retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Microcebus murinus ENSMICG000000103814 retrocopies
retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus ENSMLUG000000068651 retrocopy
retro_mluc_84,
Oryctolagus cuniculus ENSOCUG000000140435 retrocopies
retro_ocun_1100, retro_ocun_1650, retro_ocun_1869, retro_ocun_334, retro_ocun_398,
Otolemur garnettii ENSOGAG0000000875411 retrocopies
retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Pongo abelii ENSPPYG000000143282 retrocopies
retro_pabe_2126, retro_pabe_44,
Pan troglodytes ENSPTRG000000300467 retrocopies
retro_ptro_1374, retro_ptro_1719, retro_ptro_2370, retro_ptro_2927, retro_ptro_404, retro_ptro_429, retro_ptro_907,
Tupaia belangeri ENSTBEG0000001508927 retrocopies
retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,

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 = 0.43 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .22 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .26 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .15 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .13 RPM
GBR_HG00114 0 .29 RPM
GBR_HG00119 0 .34 RPM
GBR_HG00131 0 .43 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .34 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .15 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .17 RPM
TSI_NA20786 0 .16 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .24 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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