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generated an Xpd knock-in allele with a point mutation encoding a single amino acid change (XPDG602D) found in the XPCS patient XPCS2 (Figure 1A–1C). mRNA expression from the targeted allele could be detected in embryonic stem cells by RT-PCR (Figure 1D), although expression was reduced approximately 5-fold relative to wt mRNA transcript levels as determined by Northern blotting of RNA from the testis of heterozygous animals (Figure 1E). Because patient XPCS2 was a hemizygote with mutant XPD protein (XPDG602D) expressed from a single allele, the corresponding mutation was expected to be viable in the homozygous state. However, homozygous mutant mice were not observed, neither amongst live births nor embryonic day 13.5 (E13.5) or E3.5 embryos (Table 1). The corresponding hypomorphic, mutant allele was thus designated as homozygous lethal (†XPCS). Homozygous lethality of the XPCS allele is likely due to reduced levels of expression of this essential protein as a result of gene targeting (Figure 1A) rather than to the mutation itself. Xpd ablation (XpdKO /KO ) is similarly incompatible with life beyond the earliest stages of embryogenesis [22]. Consistent with this interpretation, a different targeted Xpd mutation encoding XPDR683W, which is associated with XP in the homozygous state in humans, was similarly underexpressed and lethal in the homozygous state (designated as †XP allele) (Figure 1A–1C; Table 1; unpublished data). Also, a different targeting approach leading to the use of the native 3′UTR and removal of the neo gene resulted in normalisation of XpdXPCS mRNA levels and viable homozygous XpdXPCS/XPCS (XPDG602D/G602D) animals [23]."}
craft-ca-core-dev
{"project":"craft-ca-core-dev","denotations":[{"id":"T1303","span":{"begin":16,"end":19},"obj":"PR:000007164"},{"id":"T1304","span":{"begin":29,"end":35},"obj":"SO:0001023"},{"id":"T1305","span":{"begin":95,"end":98},"obj":"PR:000007164"},{"id":"T1306","span":{"begin":158,"end":168},"obj":"GO:0010467"},{"id":"T1307","span":{"begin":187,"end":193},"obj":"SO:0001023"},{"id":"T1308","span":{"begin":215,"end":224},"obj":"UBERON:0000922"},{"id":"T1309","span":{"begin":215,"end":235},"obj":"CL:0002322"},{"id":"T1310","span":{"begin":268,"end":278},"obj":"GO:0010467"},{"id":"T1311","span":{"begin":401,"end":407},"obj":"UBERON:0000473"},{"id":"T1312","span":{"begin":424,"end":431},"obj":"NCBITaxon:33208"},{"id":"T1313","span":{"begin":496,"end":499},"obj":"PR:000007164"},{"id":"T1314","span":{"begin":509,"end":512},"obj":"PR:000007164"},{"id":"T1315","span":{"begin":519,"end":528},"obj":"GO:0010467"},{"id":"T1316","span":{"begin":543,"end":549},"obj":"SO:0001023"},{"id":"T1317","span":{"begin":656,"end":660},"obj":"NCBITaxon:10088"},{"id":"T1318","span":{"begin":712,"end":721},"obj":"UBERON:0000922"},{"id":"T1319","span":{"begin":747,"end":754},"obj":"UBERON:0000922"},{"id":"T1320","span":{"begin":804,"end":810},"obj":"SO:0001023"},{"id":"T1321","span":{"begin":894,"end":900},"obj":"SO:0001023"},{"id":"T1322","span":{"begin":936,"end":946},"obj":"GO:0010467"},{"id":"T1323","span":{"begin":988,"end":992},"obj":"SO:0000704"},{"id":"T1324","span":{"begin":1051,"end":1054},"obj":"PR:000007164"},{"id":"T1325","span":{"begin":1065,"end":1068},"obj":"PR:000007164"},{"id":"T1326","span":{"begin":1108,"end":1112},"obj":"UBERON:0000104"},{"id":"T1327","span":{"begin":1143,"end":1156},"obj":"GO:0009790"},{"id":"T1328","span":{"begin":1221,"end":1224},"obj":"PR:000007164"},{"id":"T1329","span":{"begin":1243,"end":1246},"obj":"PR:000007164"},{"id":"T1330","span":{"begin":1308,"end":1314},"obj":"NCBITaxon:9606"},{"id":"T1331","span":{"begin":1335,"end":1344},"obj":"GO:0010467"},{"id":"T1332","span":{"begin":1399,"end":1405},"obj":"SO:0001023"},{"id":"T1333","span":{"begin":1520,"end":1525},"obj":"SO:0000205"},{"id":"T1334","span":{"begin":1549,"end":1553},"obj":"SO:0000704"},{"id":"T1335","span":{"begin":1583,"end":1586},"obj":"PR:000007164"},{"id":"T1336","span":{"begin":1625,"end":1628},"obj":"PR:000007164"},{"id":"T1337","span":{"begin":1639,"end":1642},"obj":"PR:000007164"},{"id":"T1338","span":{"begin":1655,"end":1662},"obj":"NCBITaxon:33208"}],"text":"We generated an Xpd knock-in allele with a point mutation encoding a single amino acid change (XPDG602D) found in the XPCS patient XPCS2 (Figure 1A–1C). mRNA expression from the targeted allele could be detected in embryonic stem cells by RT-PCR (Figure 1D), although expression was reduced approximately 5-fold relative to wt mRNA transcript levels as determined by Northern blotting of RNA from the testis of heterozygous animals (Figure 1E). Because patient XPCS2 was a hemizygote with mutant XPD protein (XPDG602D) expressed from a single allele, the corresponding mutation was expected to be viable in the homozygous state. However, homozygous mutant mice were not observed, neither amongst live births nor embryonic day 13.5 (E13.5) or E3.5 embryos (Table 1). The corresponding hypomorphic, mutant allele was thus designated as homozygous lethal (†XPCS). Homozygous lethality of the XPCS allele is likely due to reduced levels of expression of this essential protein as a result of gene targeting (Figure 1A) rather than to the mutation itself. Xpd ablation (XpdKO /KO ) is similarly incompatible with life beyond the earliest stages of embryogenesis [22]. Consistent with this interpretation, a different targeted Xpd mutation encoding XPDR683W, which is associated with XP in the homozygous state in humans, was similarly underexpressed and lethal in the homozygous state (designated as †XP allele) (Figure 1A–1C; Table 1; unpublished data). Also, a different targeting approach leading to the use of the native 3′UTR and removal of the neo gene resulted in normalisation of XpdXPCS mRNA levels and viable homozygous XpdXPCS/XPCS (XPDG602D/G602D) animals [23]."}
craft-ca-core-ex-dev
{"project":"craft-ca-core-ex-dev","denotations":[{"id":"T1340","span":{"begin":16,"end":19},"obj":"PR_EXT:000007164"},{"id":"T1341","span":{"begin":29,"end":35},"obj":"SO_EXT:0001023"},{"id":"T1342","span":{"begin":43,"end":57},"obj":"SO_EXT:point_mutation_entity_or_process"},{"id":"T1343","span":{"begin":58,"end":66},"obj":"SO_EXT:sequence_coding_function"},{"id":"T1344","span":{"begin":76,"end":86},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1345","span":{"begin":87,"end":93},"obj":"SO_EXT:sequence_alteration_entity_or_process"},{"id":"T1346","span":{"begin":95,"end":98},"obj":"PR_EXT:000007164"},{"id":"T1347","span":{"begin":153,"end":157},"obj":"CHEBI_SO_EXT:mRNA"},{"id":"T1348","span":{"begin":158,"end":168},"obj":"GO:0010467"},{"id":"T1349","span":{"begin":187,"end":193},"obj":"SO_EXT:0001023"},{"id":"T1350","span":{"begin":215,"end":224},"obj":"UBERON:0000922"},{"id":"T1351","span":{"begin":215,"end":235},"obj":"CL:0002322"},{"id":"T1352","span":{"begin":230,"end":235},"obj":"CL_GO_EXT:cell"},{"id":"T1353","span":{"begin":239,"end":241},"obj":"GO_EXT:reverse_transcription_or_reverse_transcriptase"},{"id":"T1354","span":{"begin":268,"end":278},"obj":"GO:0010467"},{"id":"T1355","span":{"begin":324,"end":326},"obj":"SO_EXT:wild_type_entity_or_quality"},{"id":"T1356","span":{"begin":327,"end":331},"obj":"CHEBI_SO_EXT:mRNA"},{"id":"T1357","span":{"begin":388,"end":391},"obj":"CHEBI_SO_EXT:RNA"},{"id":"T1358","span":{"begin":401,"end":407},"obj":"UBERON:0000473"},{"id":"T1359","span":{"begin":424,"end":431},"obj":"NCBITaxon:33208"},{"id":"T1360","span":{"begin":489,"end":495},"obj":"SO_EXT:sequence_altered_entity_or_alteration_process"},{"id":"T1361","span":{"begin":496,"end":499},"obj":"PR_EXT:000007164"},{"id":"T1362","span":{"begin":500,"end":507},"obj":"CHEBI_PR_EXT:protein"},{"id":"T1363","span":{"begin":509,"end":512},"obj":"PR_EXT:000007164"},{"id":"T1364","span":{"begin":519,"end":528},"obj":"GO:0010467"},{"id":"T1365","span":{"begin":543,"end":549},"obj":"SO_EXT:0001023"},{"id":"T1366","span":{"begin":569,"end":577},"obj":"SO_EXT:sequence_alteration_entity_or_process"},{"id":"T1367","span":{"begin":649,"end":655},"obj":"SO_EXT:sequence_altered_entity_or_alteration_process"},{"id":"T1368","span":{"begin":656,"end":660},"obj":"NCBITaxon:10088"},{"id":"T1369","span":{"begin":712,"end":721},"obj":"UBERON:0000922"},{"id":"T1370","span":{"begin":747,"end":754},"obj":"UBERON:0000922"},{"id":"T1371","span":{"begin":797,"end":803},"obj":"SO_EXT:sequence_altered_entity_or_alteration_process"},{"id":"T1372","span":{"begin":804,"end":810},"obj":"SO_EXT:0001023"},{"id":"T1373","span":{"begin":845,"end":851},"obj":"GO_EXT:fatality_or_lethality"},{"id":"T1374","span":{"begin":872,"end":881},"obj":"GO_EXT:fatality_or_lethality"},{"id":"T1375","span":{"begin":894,"end":900},"obj":"SO_EXT:0001023"},{"id":"T1376","span":{"begin":936,"end":946},"obj":"GO:0010467"},{"id":"T1377","span":{"begin":965,"end":972},"obj":"CHEBI_PR_EXT:protein"},{"id":"T1378","span":{"begin":988,"end":992},"obj":"SO_EXT:0000704"},{"id":"T1379","span":{"begin":1034,"end":1042},"obj":"SO_EXT:sequence_alteration_entity_or_process"},{"id":"T1380","span":{"begin":1051,"end":1054},"obj":"PR_EXT:000007164"},{"id":"T1381","span":{"begin":1065,"end":1068},"obj":"PR_EXT:000007164"},{"id":"T1382","span":{"begin":1108,"end":1112},"obj":"UBERON:0000104"},{"id":"T1383","span":{"begin":1143,"end":1156},"obj":"GO:0009790"},{"id":"T1384","span":{"begin":1221,"end":1224},"obj":"PR_EXT:000007164"},{"id":"T1385","span":{"begin":1225,"end":1233},"obj":"SO_EXT:sequence_alteration_entity_or_process"},{"id":"T1386","span":{"begin":1234,"end":1242},"obj":"SO_EXT:sequence_coding_function"},{"id":"T1387","span":{"begin":1243,"end":1246},"obj":"PR_EXT:000007164"},{"id":"T1388","span":{"begin":1308,"end":1314},"obj":"NCBITaxon:9606"},{"id":"T1389","span":{"begin":1335,"end":1344},"obj":"GO:0010467"},{"id":"T1390","span":{"begin":1349,"end":1355},"obj":"GO_EXT:fatality_or_lethality"},{"id":"T1391","span":{"begin":1399,"end":1405},"obj":"SO_EXT:0001023"},{"id":"T1392","span":{"begin":1520,"end":1525},"obj":"SO_EXT:0000205"},{"id":"T1393","span":{"begin":1545,"end":1548},"obj":"CHEBI_GO_EXT:neomycin_or_neomycin_phosphotransferase"},{"id":"T1394","span":{"begin":1549,"end":1553},"obj":"SO_EXT:0000704"},{"id":"T1395","span":{"begin":1583,"end":1586},"obj":"PR_EXT:000007164"},{"id":"T1396","span":{"begin":1591,"end":1595},"obj":"CHEBI_SO_EXT:mRNA"},{"id":"T1397","span":{"begin":1625,"end":1628},"obj":"PR_EXT:000007164"},{"id":"T1398","span":{"begin":1639,"end":1642},"obj":"PR_EXT:000007164"},{"id":"T1399","span":{"begin":1655,"end":1662},"obj":"NCBITaxon:33208"}],"text":"We generated an Xpd knock-in allele with a point mutation encoding a single amino acid change (XPDG602D) found in the XPCS patient XPCS2 (Figure 1A–1C). mRNA expression from the targeted allele could be detected in embryonic stem cells by RT-PCR (Figure 1D), although expression was reduced approximately 5-fold relative to wt mRNA transcript levels as determined by Northern blotting of RNA from the testis of heterozygous animals (Figure 1E). Because patient XPCS2 was a hemizygote with mutant XPD protein (XPDG602D) expressed from a single allele, the corresponding mutation was expected to be viable in the homozygous state. However, homozygous mutant mice were not observed, neither amongst live births nor embryonic day 13.5 (E13.5) or E3.5 embryos (Table 1). The corresponding hypomorphic, mutant allele was thus designated as homozygous lethal (†XPCS). Homozygous lethality of the XPCS allele is likely due to reduced levels of expression of this essential protein as a result of gene targeting (Figure 1A) rather than to the mutation itself. Xpd ablation (XpdKO /KO ) is similarly incompatible with life beyond the earliest stages of embryogenesis [22]. Consistent with this interpretation, a different targeted Xpd mutation encoding XPDR683W, which is associated with XP in the homozygous state in humans, was similarly underexpressed and lethal in the homozygous state (designated as †XP allele) (Figure 1A–1C; Table 1; unpublished data). Also, a different targeting approach leading to the use of the native 3′UTR and removal of the neo gene resulted in normalisation of XpdXPCS mRNA levels and viable homozygous XpdXPCS/XPCS (XPDG602D/G602D) animals [23]."}
2_test
{"project":"2_test","denotations":[{"id":"17020410-9426063-84795139","span":{"begin":1158,"end":1160},"obj":"9426063"},{"id":"17020410-16904611-84795140","span":{"begin":1664,"end":1666},"obj":"16904611"},{"id":"T67903","span":{"begin":1158,"end":1160},"obj":"9426063"},{"id":"T71501","span":{"begin":1664,"end":1666},"obj":"16904611"}],"text":"We generated an Xpd knock-in allele with a point mutation encoding a single amino acid change (XPDG602D) found in the XPCS patient XPCS2 (Figure 1A–1C). mRNA expression from the targeted allele could be detected in embryonic stem cells by RT-PCR (Figure 1D), although expression was reduced approximately 5-fold relative to wt mRNA transcript levels as determined by Northern blotting of RNA from the testis of heterozygous animals (Figure 1E). Because patient XPCS2 was a hemizygote with mutant XPD protein (XPDG602D) expressed from a single allele, the corresponding mutation was expected to be viable in the homozygous state. However, homozygous mutant mice were not observed, neither amongst live births nor embryonic day 13.5 (E13.5) or E3.5 embryos (Table 1). The corresponding hypomorphic, mutant allele was thus designated as homozygous lethal (†XPCS). Homozygous lethality of the XPCS allele is likely due to reduced levels of expression of this essential protein as a result of gene targeting (Figure 1A) rather than to the mutation itself. Xpd ablation (XpdKO /KO ) is similarly incompatible with life beyond the earliest stages of embryogenesis [22]. Consistent with this interpretation, a different targeted Xpd mutation encoding XPDR683W, which is associated with XP in the homozygous state in humans, was similarly underexpressed and lethal in the homozygous state (designated as †XP allele) (Figure 1A–1C; Table 1; unpublished data). Also, a different targeting approach leading to the use of the native 3′UTR and removal of the neo gene resulted in normalisation of XpdXPCS mRNA levels and viable homozygous XpdXPCS/XPCS (XPDG602D/G602D) animals [23]."}