RetrogeneDB ID:

retro_hsap_917

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:93731808..93732392(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000256752
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HPRT1
Ensembl ID:ENSG00000165704
Aliases:HPRT1, HGPRT, HPRT
Description:hypoxanthine phosphoribosyltransferase 1 [Source:HGNC Symbol;Acc:5157]


Retrocopy-Parental alignment summary:






>retro_hsap_917
ATTGTTACCCACAGCCCCAGCATCATGATTAGTGATGATGAACCAGGTTATAACCTAGATTTATATCATATACCTCATCA
TTACACTGAGGATTTGCAAAAGGTTTTATTCCTCATGGACTGATTGTGAACAGGACCAAACGACTTGCCTGAGATGTGAT
GAAGGAGATAGGAGCCTCTCACATTGTAGCCTTCTGTTTGTTCAAGGGGGGTTGTACTTTTTTTGCTGACCTGCTAGATA
ACATCAAAGCACCTGAATAGAAATAGTCATAGAGCCATTCCTATGATAGAGCCAATACAGAGCAAGGAGCTACTGTAATG
ACCAGTCAACAGGGGATATAAAGGTAATTGGTGGCGATGATCCTTCAACTTTAACTAGAAAGAATGTCTTGATTTTTGAA
GATGTAATTGACACTGGCAAAACAATGCCAACCTTGCCTTCTGGGTCAAGTACTATAATCTAAAAATGGTCAAGGTTTGC
AAGCTCGCTAGTGAGAAAGCACCCTTCAGAGTGTTAGAAATAGGCCAGACTTTGTTGGATTTGAAATTCCAGACAAACTT
GTTGCAGGATATGCCCTTTTCTAT

ORF - retro_hsap_917 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.65 %
Parental protein coverage: 89.45 %
Number of stop codons detected: 1
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMATRSPGVVISDDEPGYDLDLFCIPNHYAEDLERV-FIPHGLIMDRTERLARDVMKEMGGHHIVALCVLK
..T.SP...ISDDEPGY.LDL..IP.HY.EDL..V.FIPHGLI..RT.RLA.DVMKE.G..HIVA.C..K
RetrocopyIVTHSPSIMISDDEPGYNLDLYHIPHHYTEDLQKV<FIPHGLIVNRTKRLA*DVMKEIGASHIVAFCLFK
ParentalGGYKFFADLLDYIKA-LNRNSDRSIPMTVDFIRLK-SYCNDQSTGDIKVIGGDDLSTLTGKNVLIVEDII
GG..FFADLLD.IKA.LNRNS.R.IPM....I..K.SYCNDQSTGDIKVIGGDD.STLT.KNVLI.ED.I
RetrocopyGGCTFFADLLDNIKA>LNRNSHRAIPM-IEPIQSK>SYCNDQSTGDIKVIGGDDPSTLTRKNVLIFEDVI
ParentalDTGKTMQTLLS-LVRQYNPKMVKV-ASLLVKRTP-RSVGYKPDFVGFEIPDKFVVGYALDY
DTGKTM.TL.S..V..YN.KMVKV.AS.LV...P..SV...PDFVGFEIPDK.V.GYAL.Y
RetrocopyDTGKTMPTLPS<WVKYYNLKMVKV>ASSLVRKHP>QSVRNRPDFVGFEIPDKLVAGYALFY

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 19 .24 RPM
bodymap2_adrenal 0 .00 RPM 28 .31 RPM
bodymap2_brain 0 .00 RPM 91 .79 RPM
bodymap2_breast 0 .00 RPM 15 .76 RPM
bodymap2_colon 0 .00 RPM 22 .93 RPM
bodymap2_heart 0 .00 RPM 13 .66 RPM
bodymap2_kidney 0 .00 RPM 55 .69 RPM
bodymap2_liver 0 .00 RPM 11 .30 RPM
bodymap2_lung 0 .00 RPM 31 .45 RPM
bodymap2_lymph_node 0 .00 RPM 19 .48 RPM
bodymap2_ovary 0 .00 RPM 41 .12 RPM
bodymap2_prostate 0 .00 RPM 22 .05 RPM
bodymap2_skeletal_muscle 0 .00 RPM 16 .10 RPM
bodymap2_testis 0 .00 RPM 90 .59 RPM
bodymap2_thyroid 0 .00 RPM 36 .36 RPM
bodymap2_white_blood_cells 0 .00 RPM 32 .27 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_917 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_917 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_917 retrocopy 5' end.

Lab - click to see more details

retro_hsap_917 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_917 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_636
Gorilla gorilla retro_ggor_740
Parental genes homology:
Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013391 retrocopy
retro_amel_129,
Bos taurus ENSBTAG000000146853 retrocopies
retro_btau_162, retro_btau_179, retro_btau_721,
Canis familiaris ENSCAFG000000188701 retrocopy
retro_cfam_2014,
Cavia porcellus ENSCPOG000000025121 retrocopy
retro_cpor_1299,
Dasypus novemcinctus ENSDNOG000000084955 retrocopies
retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Equus caballus ENSECAG000000175341 retrocopy
retro_ecab_734,
Felis catus ENSFCAG000000045752 retrocopies
retro_fcat_104, retro_fcat_1608,
Homo sapiens ENSG00000165704 1 retrocopy
retro_hsap_917 ,
Gorilla gorilla ENSGGOG000000080501 retrocopy
retro_ggor_740,
Loxodonta africana ENSLAFG000000098922 retrocopies
retro_lafr_1042, retro_lafr_475,
Microcebus murinus ENSMICG000000065471 retrocopy
retro_mmur_1186,
Myotis lucifugus ENSMLUG000000035911 retrocopy
retro_mluc_2107,
Macaca mulatta ENSMMUG000000083031 retrocopy
retro_mmul_1118,
Mustela putorius furoENSMPUG000000126993 retrocopies
retro_mputfur_1317, retro_mputfur_1638, retro_mputfur_836,
Oryctolagus cuniculus ENSOCUG000000031861 retrocopy
retro_ocun_1082,
Otolemur garnettii ENSOGAG000000038813 retrocopies
retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii ENSPPYG000000207332 retrocopies
retro_pabe_3601, retro_pabe_791,
Pan troglodytes ENSPTRG000000222872 retrocopies
retro_ptro_2042, retro_ptro_636,
Rattus norvegicus ENSRNOG000000313672 retrocopies
retro_rnor_1208, retro_rnor_2491,
Sarcophilus harrisii ENSSHAG000000079653 retrocopies
retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri ENSTBEG000000008595 retrocopies
retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta ENSTSYG000000095791 retrocopy
retro_tsyr_2050,
Tursiops truncatus ENSTTRG000000099549 retrocopies
retro_ttru_1007, retro_ttru_1272, retro_ttru_1523, retro_ttru_1598, retro_ttru_1620, retro_ttru_276, retro_ttru_641, retro_ttru_732, retro_ttru_829,
Vicugna pacos ENSVPAG000000091331 retrocopy
retro_vpac_122,

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 ) 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 .00 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).





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