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PCR\nTo check that the Homer3, Dncl1 and Trim11 clones were not identified multiple times solely because they are highly abundant in the library, we performed a semi-quantitative PCR assay. We compared the relative abundance of Homer3, Dncl1, Trim11 and Pax6 with Gapdh and Atp5a1. Gapdh and Atp5a1 both show strong constitutive expression in a variety of tissues including the brain [29,30]. Homer3, Dncl1, Trim11 and Pax6 were only amplified strongly after 35 cycles of PCR (Figure 2) and were therefore present at relatively low levels compared to Gapdh (amplified strongly after 25 cycles) and Atp5a1 (amplified strongly after 30 cycles; Figure 2).\nFigure 2 Semi-quantitative PCR analysis of Homer3, Dncl1, Trim11 and Pax6 in the mouse brain cDNA library. Library cDNA was amplified with primers specific for Pax6 (600 bp), Homer3 (485 bp band), Dncl1 (485 bp) and Trim11 (609 bp) for 20, 25, 30 or 35 cycles. Atp5a1 (415 bp) and Gapdh (450 bp), which are highly expressed in the brain, are included for comparison. M indicates the Φ×174 HaeIII DNA size marker; the positions of the 603 bp and 310 bp marker bands are indicated. We concluded that Homer3, Dncl1 and Trim11 clones were not highly abundant in the library. This is consistent with the idea that they were pulled out because the encoded proteins interact specifically with the C-terminal peptide or PST domain of PAX6."}

{"project":"craft-ca-core-ex-dev","denotations":[{"id":"T2808","span":{"begin":40,"end":46},"obj":"PR_EXT:000008680"},{"id":"T2809","span":{"begin":48,"end":53},"obj":"PR_EXT:000002325"},{"id":"T2810","span":{"begin":58,"end":64},"obj":"PR_EXT:000016642"},{"id":"T2811","span":{"begin":65,"end":71},"obj":"SO_EXT:sequence_cloned_entity"},{"id":"T2812","span":{"begin":245,"end":251},"obj":"PR_EXT:000008680"},{"id":"T2813","span":{"begin":253,"end":258},"obj":"PR_EXT:000002325"},{"id":"T2814","span":{"begin":260,"end":266},"obj":"PR_EXT:000016642"},{"id":"T2815","span":{"begin":271,"end":275},"obj":"PR_EXT:000012318"},{"id":"T2816","span":{"begin":281,"end":286},"obj":"GO_PR_EXT:glyceraldehyde_3_phosphate_dehydrogenase"},{"id":"T8439","span":{"begin":714,"end":720},"obj":"PR_EXT:000008680"},{"id":"T8440","span":{"begin":722,"end":727},"obj":"PR_EXT:000002325"},{"id":"T8441","span":{"begin":729,"end":735},"obj":"PR_EXT:000016642"},{"id":"T8442","span":{"begin":740,"end":744},"obj":"PR_EXT:000012318"},{"id":"T8443","span":{"begin":752,"end":757},"obj":"NCBITaxon:10088"},{"id":"T8444","span":{"begin":758,"end":763},"obj":"UBERON:0000955"},{"id":"T8445","span":{"begin":764,"end":768},"obj":"SO_EXT:cDNA"},{"id":"T8446","span":{"begin":786,"end":790},"obj":"SO_EXT:cDNA"},{"id":"T8447","span":{"begin":810,"end":817},"obj":"SO_EXT:0000112"},{"id":"T8448","span":{"begin":831,"end":835},"obj":"PR_EXT:000012318"},{"id":"T8449","span":{"begin":841,"end":843},"obj":"SO_EXT:0000028"},{"id":"T8450","span":{"begin":846,"end":852},"obj":"PR_EXT:000008680"},{"id":"T8451","span":{"begin":858,"end":860},"obj":"SO_EXT:0000028"},{"id":"T8452","span":{"begin":868,"end":873},"obj":"PR_EXT:000002325"},{"id":"T8453","span":{"begin":879,"end":881},"obj":"SO_EXT:0000028"},{"id":"T8454","span":{"begin":887,"end":893},"obj":"PR_EXT:000016642"},{"id":"T8455","span":{"begin":899,"end":901},"obj":"SO_EXT:0000028"},{"id":"T8456","span":{"begin":932,"end":938},"obj":"PR_EXT:000004453"},{"id":"T8457","span":{"begin":944,"end":946},"obj":"SO_EXT:0000028"},{"id":"T8458","span":{"begin":952,"end":957},"obj":"GO_PR_EXT:glyceraldehyde_3_phosphate_dehydrogenase"},{"id":"T8459","span":{"begin":963,"end":965},"obj":"SO_EXT:0000028"},{"id":"T8460","span":{"begin":985,"end":994},"obj":"GO:0010467"},{"id":"T8461","span":{"begin":1002,"end":1007},"obj":"UBERON:0000955"},{"id":"T8462","span":{"begin":1054,"end":1059},"obj":"NCBITaxon:1910954"},{"id":"T8463","span":{"begin":1067,"end":1070},"obj":"CHEBI_SO_EXT:DNA"},{"id":"T8464","span":{"begin":1076,"end":1082},"obj":"CHEBI_SO_EXT:molecular_indicator_or_label_or_marker_or_tag"},{"id":"T8465","span":{"begin":1109,"end":1111},"obj":"SO_EXT:0000028"},{"id":"T8466","span":{"begin":1120,"end":1122},"obj":"SO_EXT:0000028"},{"id":"T8467","span":{"begin":1123,"end":1129},"obj":"CHEBI_SO_EXT:molecular_indicator_or_label_or_marker_or_tag"},{"id":"T2817","span":{"begin":291,"end":297},"obj":"PR_EXT:000004453"},{"id":"T2818","span":{"begin":299,"end":304},"obj":"GO_PR_EXT:glyceraldehyde_3_phosphate_dehydrogenase"},{"id":"T2819","span":{"begin":309,"end":315},"obj":"PR_EXT:000004453"},{"id":"T2820","span":{"begin":346,"end":356},"obj":"GO:0010467"},{"id":"T2821","span":{"begin":373,"end":380},"obj":"UBERON:0000479"},{"id":"T2822","span":{"begin":395,"end":400},"obj":"UBERON:0000955"},{"id":"T2823","span":{"begin":410,"end":416},"obj":"PR_EXT:000008680"},{"id":"T2824","span":{"begin":418,"end":423},"obj":"PR_EXT:000002325"},{"id":"T2825","span":{"begin":425,"end":431},"obj":"PR_EXT:000016642"},{"id":"T2826","span":{"begin":436,"end":440},"obj":"PR_EXT:000012318"},{"id":"T2827","span":{"begin":568,"end":573},"obj":"GO_PR_EXT:glyceraldehyde_3_phosphate_dehydrogenase"},{"id":"T2828","span":{"begin":615,"end":621},"obj":"PR_EXT:000004453"},{"id":"T2829","span":{"begin":1169,"end":1175},"obj":"PR_EXT:000008680"},{"id":"T2830","span":{"begin":1177,"end":1182},"obj":"PR_EXT:000002325"},{"id":"T2831","span":{"begin":1187,"end":1193},"obj":"PR_EXT:000016642"},{"id":"T2832","span":{"begin":1194,"end":1200},"obj":"SO_EXT:sequence_cloned_entity"},{"id":"T2833","span":{"begin":1313,"end":1320},"obj":"SO_EXT:sequence_coding_function"},{"id":"T2834","span":{"begin":1321,"end":1329},"obj":"CHEBI_PR_EXT:protein"},{"id":"T2835","span":{"begin":1361,"end":1371},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T2836","span":{"begin":1372,"end":1379},"obj":"CHEBI_SO_EXT:peptide_or_peptide_region"},{"id":"T2837","span":{"begin":1387,"end":1393},"obj":"SO_EXT:0000417"},{"id":"T2838","span":{"begin":1397,"end":1401},"obj":"PR_EXT:000012318"}],"text":"Semi-quantitative PCR\nTo check that the Homer3, Dncl1 and Trim11 clones were not identified multiple times solely because they are highly abundant in the library, we performed a semi-quantitative PCR assay. We compared the relative abundance of Homer3, Dncl1, Trim11 and Pax6 with Gapdh and Atp5a1. Gapdh and Atp5a1 both show strong constitutive expression in a variety of tissues including the brain [29,30]. Homer3, Dncl1, Trim11 and Pax6 were only amplified strongly after 35 cycles of PCR (Figure 2) and were therefore present at relatively low levels compared to Gapdh (amplified strongly after 25 cycles) and Atp5a1 (amplified strongly after 30 cycles; Figure 2).\nFigure 2 Semi-quantitative PCR analysis of Homer3, Dncl1, Trim11 and Pax6 in the mouse brain cDNA library. Library cDNA was amplified with primers specific for Pax6 (600 bp), Homer3 (485 bp band), Dncl1 (485 bp) and Trim11 (609 bp) for 20, 25, 30 or 35 cycles. Atp5a1 (415 bp) and Gapdh (450 bp), which are highly expressed in the brain, are included for comparison. M indicates the Φ×174 HaeIII DNA size marker; the positions of the 603 bp and 310 bp marker bands are indicated. We concluded that Homer3, Dncl1 and Trim11 clones were not highly abundant in the library. This is consistent with the idea that they were pulled out because the encoded proteins interact specifically with the C-terminal peptide or PST domain of PAX6."}

{"project":"craft-ca-core-dev","denotations":[{"id":"T2786","span":{"begin":40,"end":46},"obj":"PR:000008680"},{"id":"T2787","span":{"begin":48,"end":53},"obj":"PR:000002325"},{"id":"T2788","span":{"begin":58,"end":64},"obj":"PR:000016642"},{"id":"T2789","span":{"begin":245,"end":251},"obj":"PR:000008680"},{"id":"T2790","span":{"begin":253,"end":258},"obj":"PR:000002325"},{"id":"T2797","span":{"begin":395,"end":400},"obj":"UBERON:0000955"},{"id":"T2798","span":{"begin":410,"end":416},"obj":"PR:000008680"},{"id":"T2799","span":{"begin":418,"end":423},"obj":"PR:000002325"},{"id":"T2800","span":{"begin":425,"end":431},"obj":"PR:000016642"},{"id":"T2801","span":{"begin":436,"end":440},"obj":"PR:000012318"},{"id":"T2802","span":{"begin":615,"end":621},"obj":"PR:000004453"},{"id":"T2803","span":{"begin":1169,"end":1175},"obj":"PR:000008680"},{"id":"T2804","span":{"begin":1177,"end":1182},"obj":"PR:000002325"},{"id":"T2805","span":{"begin":1187,"end":1193},"obj":"PR:000016642"},{"id":"T2806","span":{"begin":1387,"end":1393},"obj":"SO:0000417"},{"id":"T2807","span":{"begin":1397,"end":1401},"obj":"PR:000012318"},{"id":"T8416","span":{"begin":714,"end":720},"obj":"PR:000008680"},{"id":"T8417","span":{"begin":722,"end":727},"obj":"PR:000002325"},{"id":"T8418","span":{"begin":729,"end":735},"obj":"PR:000016642"},{"id":"T8419","span":{"begin":740,"end":744},"obj":"PR:000012318"},{"id":"T8420","span":{"begin":752,"end":757},"obj":"NCBITaxon:10088"},{"id":"T8421","span":{"begin":758,"end":763},"obj":"UBERON:0000955"},{"id":"T8422","span":{"begin":810,"end":817},"obj":"SO:0000112"},{"id":"T8423","span":{"begin":831,"end":835},"obj":"PR:000012318"},{"id":"T8424","span":{"begin":841,"end":843},"obj":"SO:0000028"},{"id":"T8425","span":{"begin":846,"end":852},"obj":"PR:000008680"},{"id":"T8426","span":{"begin":858,"end":860},"obj":"SO:0000028"},{"id":"T8427","span":{"begin":868,"end":873},"obj":"PR:000002325"},{"id":"T8428","span":{"begin":879,"end":881},"obj":"SO:0000028"},{"id":"T8429","span":{"begin":887,"end":893},"obj":"PR:000016642"},{"id":"T8430","span":{"begin":899,"end":901},"obj":"SO:0000028"},{"id":"T8431","span":{"begin":932,"end":938},"obj":"PR:000004453"},{"id":"T8432","span":{"begin":944,"end":946},"obj":"SO:0000028"},{"id":"T8433","span":{"begin":963,"end":965},"obj":"SO:0000028"},{"id":"T8434","span":{"begin":985,"end":994},"obj":"GO:0010467"},{"id":"T8435","span":{"begin":1002,"end":1007},"obj":"UBERON:0000955"},{"id":"T8436","span":{"begin":1054,"end":1059},"obj":"NCBITaxon:1910954"},{"id":"T8437","span":{"begin":1109,"end":1111},"obj":"SO:0000028"},{"id":"T8438","span":{"begin":1120,"end":1122},"obj":"SO:0000028"},{"id":"T2791","span":{"begin":260,"end":266},"obj":"PR:000016642"},{"id":"T2792","span":{"begin":271,"end":275},"obj":"PR:000012318"},{"id":"T2793","span":{"begin":291,"end":297},"obj":"PR:000004453"},{"id":"T2794","span":{"begin":309,"end":315},"obj":"PR:000004453"},{"id":"T2795","span":{"begin":346,"end":356},"obj":"GO:0010467"},{"id":"T2796","span":{"begin":373,"end":380},"obj":"UBERON:0000479"}],"text":"Semi-quantitative PCR\nTo check that the Homer3, Dncl1 and Trim11 clones were not identified multiple times solely because they are highly abundant in the library, we performed a semi-quantitative PCR assay. We compared the relative abundance of Homer3, Dncl1, Trim11 and Pax6 with Gapdh and Atp5a1. Gapdh and Atp5a1 both show strong constitutive expression in a variety of tissues including the brain [29,30]. Homer3, Dncl1, Trim11 and Pax6 were only amplified strongly after 35 cycles of PCR (Figure 2) and were therefore present at relatively low levels compared to Gapdh (amplified strongly after 25 cycles) and Atp5a1 (amplified strongly after 30 cycles; Figure 2).\nFigure 2 Semi-quantitative PCR analysis of Homer3, Dncl1, Trim11 and Pax6 in the mouse brain cDNA library. Library cDNA was amplified with primers specific for Pax6 (600 bp), Homer3 (485 bp band), Dncl1 (485 bp) and Trim11 (609 bp) for 20, 25, 30 or 35 cycles. Atp5a1 (415 bp) and Gapdh (450 bp), which are highly expressed in the brain, are included for comparison. M indicates the Φ×174 HaeIII DNA size marker; the positions of the 603 bp and 310 bp marker bands are indicated. We concluded that Homer3, Dncl1 and Trim11 clones were not highly abundant in the library. This is consistent with the idea that they were pulled out because the encoded proteins interact specifically with the C-terminal peptide or PST domain of PAX6."}