RetrogeneDB ID:

retro_hsap_1666

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:14956236..14956645(-)
Located in intron of:ENSG00000103512
Retrocopy
information
Ensembl ID:ENSG00000270734
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACP1
Ensembl ID:ENSG00000143727
Aliases:ACP1, HAAP
Description:acid phosphatase 1, soluble [Source:HGNC Symbol;Acc:122]


Retrocopy-Parental alignment summary:






>retro_hsap_1666
GAACAGGGGCCCGTAGTGGGGCTGTTTGTGTGTTCCGGGTGACATCTGGCAATCCCCCACTGCAGAGGCAATTTTAAGAA
AATCTGCAGATAATAAAAACGTTTCAGGTAATTGGATCGTTGACAGCGGAGCGGCCTTGGACTGAGAATGTGGGCTAGCC
CTTAAAAGCAAGAGCTCTAAGCTGCCTAAGAAACTGTGGCATTACCAGGCCATCAAATAAGTCAGGATTATCAAAGACGT
CTTCCTTGCTTGTGATTATATATAATACATGGATGAAAGCAAACAGGGAGATTGGAACAGAAAAGGTAATTAAGTTAAAA
AATGCAAAGCTAAAATTGAACTCCTTGGGAGGTAGGAGCCACAAATGTAACTTATAACTGAAAAGCCCTATTAAGGTAAT
GCTTCAGAT

ORF - retro_hsap_1666 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.96 %
Parental protein coverage: 86.08 %
Number of stop codons detected: 7
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEQATKSVLFVCLG-NICRSPIAEAVFRKLVTDQNISENWVIDSGAVSD-WNVGRSPDPRAVSCLRNHGI-
EQ.....LFVC.G..I..SP.AEA..RK.....N.S.NW..DSGA..D..NVG.....RA.SCLRN.GI.
RetrocopyEQGPVVGLFVCSG>DIWQSPTAEAILRKSADNKNVSGNWIVDSGAALD>ENVG*PLKARALSCLRNCGI<
ParentalHTAHKARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSD
..A.K...I.K..F...DYI..MDES...D.NRK.N.VK.CKAKIELLG...PQ..LI.E.PY.GN.SD
RetrocopyYQAIK*VRIIKDVFLACDYI*YMDESKQGDWNRKGN*VKKCKAKIELLGR*EPQM*LITEKPY*GNASD

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 34 .97 RPM
bodymap2_adrenal 0 .00 RPM 60 .12 RPM
bodymap2_brain 0 .00 RPM 61 .55 RPM
bodymap2_breast 0 .00 RPM 40 .41 RPM
bodymap2_colon 0 .00 RPM 42 .79 RPM
bodymap2_heart 0 .00 RPM 45 .84 RPM
bodymap2_kidney 0 .00 RPM 79 .43 RPM
bodymap2_liver 0 .00 RPM 48 .01 RPM
bodymap2_lung 0 .00 RPM 51 .25 RPM
bodymap2_lymph_node 0 .00 RPM 56 .48 RPM
bodymap2_ovary 0 .00 RPM 60 .86 RPM
bodymap2_prostate 0 .00 RPM 61 .45 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .47 RPM
bodymap2_testis 0 .02 RPM 88 .80 RPM
bodymap2_thyroid 0 .00 RPM 88 .68 RPM
bodymap2_white_blood_cells 0 .10 RPM 61 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1666 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1666 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1666 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1666 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1666 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 30 parental genes, and 270 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095542 retrocopies
retro_amel_705, retro_amel_761,
Bos taurus ENSBTAG000000204984 retrocopies
retro_btau_1085, retro_btau_1099, retro_btau_1695, retro_btau_421,
Canis familiaris ENSCAFG000000300971 retrocopy
retro_cfam_1126,
Choloepus hoffmanni ENSCHOG0000000389194 retrocopies
retro_chof_1010, retro_chof_1053, retro_chof_1073, retro_chof_1099, retro_chof_1100, retro_chof_1144, retro_chof_119, retro_chof_1190, retro_chof_121, retro_chof_1259, retro_chof_1265, retro_chof_1275, retro_chof_1330, retro_chof_1351, retro_chof_1359, retro_chof_1389, retro_chof_1390, retro_chof_1412, retro_chof_142, retro_chof_1444, retro_chof_1447, retro_chof_1508, retro_chof_1567, retro_chof_1570, retro_chof_1593, retro_chof_1632, retro_chof_1633, retro_chof_1658, retro_chof_1684, retro_chof_169, retro_chof_1698, retro_chof_17, retro_chof_1716, retro_chof_174, retro_chof_1799, retro_chof_1802, retro_chof_1815, retro_chof_1833, retro_chof_1838, retro_chof_1864, retro_chof_1941, retro_chof_1956, retro_chof_1993, retro_chof_2012, retro_chof_2041, retro_chof_2044, retro_chof_2091, retro_chof_2165, retro_chof_2192, retro_chof_2208, retro_chof_2228, retro_chof_2259, retro_chof_2344, retro_chof_2378, retro_chof_2384, retro_chof_2443, retro_chof_245, retro_chof_2478, retro_chof_2512, retro_chof_2532, retro_chof_2542, retro_chof_2551, retro_chof_261, retro_chof_262, retro_chof_2622, retro_chof_2636, retro_chof_2643, retro_chof_2653, retro_chof_2654, retro_chof_2678, retro_chof_2701, retro_chof_2705, retro_chof_2707, retro_chof_319, retro_chof_377, retro_chof_460, retro_chof_598, retro_chof_603, retro_chof_649, retro_chof_650, retro_chof_66, retro_chof_727, retro_chof_80, retro_chof_803, retro_chof_83, retro_chof_842, retro_chof_934, retro_chof_939, retro_chof_958, retro_chof_962, retro_chof_986, retro_chof_991, retro_chof_994, retro_chof_999,
Callithrix jacchus ENSCJAG000000116635 retrocopies
retro_cjac_1226, retro_cjac_2082, retro_cjac_2162, retro_cjac_405, retro_cjac_609,
Cavia porcellus ENSCPOG000000028624 retrocopies
retro_cpor_215, retro_cpor_614, retro_cpor_678, retro_cpor_868,
Dasypus novemcinctus ENSDNOG0000001738232 retrocopies
retro_dnov_1166, retro_dnov_1213, retro_dnov_1234, retro_dnov_1255, retro_dnov_1302, retro_dnov_136, retro_dnov_1373, retro_dnov_1393, retro_dnov_1499, retro_dnov_1553, retro_dnov_1601, retro_dnov_1685, retro_dnov_1709, retro_dnov_1732, retro_dnov_1895, retro_dnov_1937, retro_dnov_1950, retro_dnov_2320, retro_dnov_2349, retro_dnov_2509, retro_dnov_2582, retro_dnov_297, retro_dnov_312, retro_dnov_355, retro_dnov_474, retro_dnov_501, retro_dnov_535, retro_dnov_650, retro_dnov_768, retro_dnov_81, retro_dnov_830, retro_dnov_987,
Dipodomys ordii ENSDORG000000164696 retrocopies
retro_dord_112, retro_dord_156, retro_dord_383, retro_dord_410, retro_dord_541, retro_dord_55,
Equus caballus ENSECAG000000100791 retrocopy
retro_ecab_135,
Echinops telfairi ENSETEG0000001376418 retrocopies
retro_etel_100, retro_etel_1034, retro_etel_110, retro_etel_1204, retro_etel_1655, retro_etel_1718, retro_etel_1824, retro_etel_1861, retro_etel_1940, retro_etel_2133, retro_etel_230, retro_etel_343, retro_etel_398, retro_etel_420, retro_etel_679, retro_etel_797, retro_etel_82, retro_etel_958,
Felis catus ENSFCAG000000267171 retrocopy
retro_fcat_1472,
Homo sapiens ENSG00000143727 5 retrocopies
retro_hsap_1627, retro_hsap_1666 , retro_hsap_1667, retro_hsap_529, retro_hsap_603,
Gorilla gorilla ENSGGOG000000155775 retrocopies
retro_ggor_1228, retro_ggor_1256, retro_ggor_485, retro_ggor_532, retro_ggor_72,
Loxodonta africana ENSLAFG000000029664 retrocopies
retro_lafr_1053, retro_lafr_1227, retro_lafr_336, retro_lafr_916,
Macropus eugenii ENSMEUG000000107333 retrocopies
retro_meug_1736, retro_meug_706, retro_meug_806,
Myotis lucifugus ENSMLUG000000177074 retrocopies
retro_mluc_133, retro_mluc_1970, retro_mluc_548, retro_mluc_686,
Macaca mulatta ENSMMUG000000170972 retrocopies
retro_mmul_1575, retro_mmul_2447,
Monodelphis domestica ENSMODG000000257643 retrocopies
retro_mdom_236, retro_mdom_292, retro_mdom_364,
Mustela putorius furoENSMPUG000000127872 retrocopies
retro_mputfur_1420, retro_mputfur_1619,
Mus musculus ENSMUSG0000004457311 retrocopies
retro_mmus_1041, retro_mmus_1103, retro_mmus_1230, retro_mmus_1261, retro_mmus_2133, retro_mmus_2143, retro_mmus_2155, retro_mmus_2969, retro_mmus_3690, retro_mmus_455, retro_mmus_717,
Nomascus leucogenys ENSNLEG000000083596 retrocopies
retro_nleu_1784, retro_nleu_2230, retro_nleu_2683, retro_nleu_2792, retro_nleu_2821, retro_nleu_2915,
Oryctolagus cuniculus ENSOCUG0000001287611 retrocopies
retro_ocun_1192, retro_ocun_1302, retro_ocun_1328, retro_ocun_1347, retro_ocun_1358, retro_ocun_1501, retro_ocun_1610, retro_ocun_1743, retro_ocun_1744, retro_ocun_1859, retro_ocun_1860,
Otolemur garnettii ENSOGAG000000003015 retrocopies
retro_ogar_1665, retro_ogar_2357, retro_ogar_3182, retro_ogar_426, retro_ogar_471,
Pongo abelii ENSPPYG000000126946 retrocopies
retro_pabe_1374, retro_pabe_1406, retro_pabe_1748, retro_pabe_220, retro_pabe_543, retro_pabe_588,
Pan troglodytes ENSPTRG000000116055 retrocopies
retro_ptro_1129, retro_ptro_2959, retro_ptro_3050, retro_ptro_3080, retro_ptro_446,
Pteropus vampyrus ENSPVAG000000133875 retrocopies
retro_pvam_1117, retro_pvam_1401, retro_pvam_28, retro_pvam_781, retro_pvam_944,
Rattus norvegicus ENSRNOG0000000526011 retrocopies
retro_rnor_1201, retro_rnor_1302, retro_rnor_1303, retro_rnor_1476, retro_rnor_1802, retro_rnor_2079, retro_rnor_2382, retro_rnor_2569, retro_rnor_2772, retro_rnor_449, retro_rnor_457,
Ictidomys tridecemlineatus ENSSTOG000000025203 retrocopies
retro_itri_1010, retro_itri_1581, retro_itri_821,
Tarsius syrichta ENSTSYG000000048647 retrocopies
retro_tsyr_1013, retro_tsyr_1214, retro_tsyr_1477, retro_tsyr_1482, retro_tsyr_209, retro_tsyr_444, retro_tsyr_523,
Tursiops truncatus ENSTTRG000000107704 retrocopies
retro_ttru_130, retro_ttru_1934, retro_ttru_293, retro_ttru_392,

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 = 0.05 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 .04 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 .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 .05 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 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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