RetrogeneDB ID:

retro_hsap_256

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:166837958..166838444(+)
Located in intron of:ENSG00000152382
Retrocopy
information
Ensembl ID:ENSG00000225171
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DUT
Ensembl ID:ENSG00000128951
Aliases:DUT, dUTPase
Description:deoxyuridine triphosphatase [Source:HGNC Symbol;Acc:3078]


Retrocopy-Parental alignment summary:






>retro_hsap_256
GGCTCTCTCAAGCCCTATTCTGAGGGACACCACTATTTCCCCCATTGAGCAAACTGGCCTGCGGGGGAGGGTGGCACACA
GAGCAGCCTTGCCCAGCTCTCCCAGCATAACACGCCCGGACCAAGGGGTCCACGGGGGCTAGGACTTGGACATGCCTAGG
ATTACACAATACCACCTAGGGAGAAAGCACTTGTGAAAACAAACATTCAGACAGTCCTTCCTTCTGGGTGTTAGAAAAGA
GTAGTGCCACATCTGGCTTGGCTGAAAAACACTTTACTGATGTAGGAGCTGGCATCATAAGATGAAGATTATAGAGGAAG
TGTTGGTGTTGTACAATTCAATTTTGGCAAAGAAAAGTTTGGTGTCAAAAATGGTGATCAAATTGCATAGCTCATTTGTG
AACAGACTTTTTCTCCAGAAACAGAAATTCAAGCTTTGGATGACACTGAAAGGGGTTCAGGAGGTTTGGGTTCCACTGGA
AAGAAT

ORF - retro_hsap_256 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.5 %
Parental protein coverage: 65.87 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGSPAPGPETPAISPSKRARPAEVGGMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKT
GS..P..E.....P.....PA..GG.Q...A.LS.H.T...RG.....G..L..A.DYTIPP.EKA.VKT
RetrocopyGSLKPYSEGHHYFPH*ANWPAGEGGTQSSLAQLSQHNTPGPRGPR---GLGLGHA*DYTIPPREKALVKT
ParentalDIQIALPSGCYGRVAPR-SGLAAKHFIDVGAGVI-DEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICER
.IQ..LPSGC..RV.P..SGLA.KHF.DVGAG.I.DEDYRG.VGVV.FNFGKEKF.VK.GD.IA.LICE.
RetrocopyNIQTVLPSGC*KRVVPH<SGLAEKHFTDVGAGII>DEDYRGSVGVVQFNFGKEKFGVKNGDQIA*LICEQ
ParentalIFYPEIEEVQALDDTERGSGGFGSTGKN
.F.PE..E.QALDDTERGSGG.GSTGKN
RetrocopyTFSPE-TEIQALDDTERGSGGLGSTGKN

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 .68 RPM 25 .66 RPM
bodymap2_adrenal 1 .43 RPM 32 .20 RPM
bodymap2_brain 0 .89 RPM 30 .57 RPM
bodymap2_breast 0 .53 RPM 37 .12 RPM
bodymap2_colon 0 .08 RPM 46 .95 RPM
bodymap2_heart 0 .17 RPM 26 .45 RPM
bodymap2_kidney 0 .06 RPM 38 .45 RPM
bodymap2_liver 0 .27 RPM 10 .60 RPM
bodymap2_lung 0 .32 RPM 35 .06 RPM
bodymap2_lymph_node 0 .02 RPM 58 .26 RPM
bodymap2_ovary 0 .66 RPM 32 .94 RPM
bodymap2_prostate 0 .17 RPM 61 .35 RPM
bodymap2_skeletal_muscle 0 .31 RPM 7 .75 RPM
bodymap2_testis 0 .62 RPM 47 .25 RPM
bodymap2_thyroid 0 .24 RPM 47 .79 RPM
bodymap2_white_blood_cells 0 .06 RPM 32 .82 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_256 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_256 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_256 retrocopy 5' end.

Lab - click to see more details

retro_hsap_256 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_256 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_216
Gorilla gorilla retro_ggor_306
Macaca mulatta retro_mmul_449
Parental genes homology:
Parental genes homology involve 24 parental genes, and 78 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000018731 retrocopy
retro_amel_1411,
Bos taurus ENSBTAG000000119983 retrocopies
retro_btau_1765, retro_btau_510, retro_btau_60,
Callithrix jacchus ENSCJAG000000018132 retrocopies
retro_cjac_1014, retro_cjac_2008,
Dasypus novemcinctus ENSDNOG000000247918 retrocopies
retro_dnov_204, retro_dnov_2096, retro_dnov_2230, retro_dnov_225, retro_dnov_2270, retro_dnov_2608, retro_dnov_528, retro_dnov_639,
Dipodomys ordii ENSDORG000000105601 retrocopy
retro_dord_146,
Equus caballus ENSECAG000000159711 retrocopy
retro_ecab_375,
Felis catus ENSFCAG000000153503 retrocopies
retro_fcat_1158, retro_fcat_33, retro_fcat_937,
Homo sapiens ENSG00000128951 6 retrocopies
retro_hsap_1698, retro_hsap_256 , retro_hsap_2699, retro_hsap_2963, retro_hsap_3624, retro_hsap_4771,
Gorilla gorilla ENSGGOG000000056585 retrocopies
retro_ggor_1272, retro_ggor_1453, retro_ggor_2053, retro_ggor_2974, retro_ggor_306,
Macropus eugenii ENSMEUG000000063183 retrocopies
retro_meug_1739, retro_meug_2104, retro_meug_476,
Myotis lucifugus ENSMLUG000000068422 retrocopies
retro_mluc_1550, retro_mluc_487,
Macaca mulatta ENSMMUG000000168986 retrocopies
retro_mmul_1429, retro_mmul_2645, retro_mmul_449, retro_mmul_707, retro_mmul_720, retro_mmul_910,
Monodelphis domestica ENSMODG000000026873 retrocopies
retro_mdom_1606, retro_mdom_1858, retro_mdom_693,
Nomascus leucogenys ENSNLEG000000059962 retrocopies
retro_nleu_2602, retro_nleu_859,
Oryctolagus cuniculus ENSOCUG000000038621 retrocopy
retro_ocun_798,
Otolemur garnettii ENSOGAG000000288477 retrocopies
retro_ogar_1207, retro_ogar_1422, retro_ogar_1500, retro_ogar_1653, retro_ogar_2348, retro_ogar_2815, retro_ogar_3485,
Pongo abelii ENSPPYG000000064542 retrocopies
retro_pabe_3820, retro_pabe_3831,
Pan troglodytes ENSPTRG000000070442 retrocopies
retro_ptro_216, retro_ptro_3177,
Rattus norvegicus ENSRNOG000000072211 retrocopy
retro_rnor_859,
Sus scrofa ENSSSCG000000260963 retrocopies
retro_sscr_1121, retro_sscr_122, retro_sscr_175,
Ictidomys tridecemlineatus ENSSTOG000000078111 retrocopy
retro_itri_125,
Tarsius syrichta ENSTSYG000000126699 retrocopies
retro_tsyr_1044, retro_tsyr_1236, retro_tsyr_1251, retro_tsyr_1825, retro_tsyr_1991, retro_tsyr_215, retro_tsyr_616, retro_tsyr_747, retro_tsyr_771,
Tursiops truncatus ENSTTRG000000154222 retrocopies
retro_ttru_1834, retro_ttru_585,
Vicugna pacos ENSVPAG000000047234 retrocopies
retro_vpac_213, retro_vpac_32, retro_vpac_527, retro_vpac_612,

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 = 0.51 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .24 RPM
CEU_NA11843 0 .31 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .22 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .30 RPM
FIN_HG00328 0 .36 RPM
FIN_HG00338 0 .17 RPM
FIN_HG00349 0 .11 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .23 RPM
GBR_HG00111 0 .21 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .22 RPM
GBR_HG00131 0 .34 RPM
GBR_HG00133 0 .51 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .36 RPM
GBR_HG00142 0 .44 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .29 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .34 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .31 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .16 RPM
YRI_NA18870 0 .17 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .19 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .24 RPM
YRI_NA19214 0 .05 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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