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of the RHAMM gene in the phylogeny of the coiled coil gene family\nHuman RHAMM has also been proposed to be the missing fourth member of the TACC family [10]. Evidence used in support of this claim included its chromosomal location on 5q32 in humans (discussed below), its sequence similarity in its coiled coil domain to the TACC domain and the subcellular localization of the RHAMM protein in the centrosome. However, if RHAMM were a bona fide TACC family member, then we would predict its evolution would be similar to those of other TACC family members, and fit with the proposed evolution of the vertebrate genome. Thus, we set out to identify RHAMM orthologues and related genes in metazoans, so that a more complete phylogeny of the coiled coil super family could be generated. We identified a single RHAMM gene in all deuterostomes for which cDNA and/or genomic sequence was available, including C. intestinalis. No RHAMM gene was identified in insects or nematodes. This indicates that the RHAMM/TACC genes diverged after the protostome/deuterostome split 833–933 MYA, but prior to the echinodermata/urochordate divergence (\u003e750 MYA). Significantly, sequence and phylogenetic analysis of coiled coil proteins (Fig. 1) clearly shows that RHAMM does not contain a TACC domain and instead forms a distinct family of proteins in the coiled coil superfamily, and is not a direct descendant of the ancestral TACC gene."}
craft-ca-core-ex-dev
{"project":"craft-ca-core-ex-dev","denotations":[{"id":"T3361","span":{"begin":17,"end":22},"obj":"PR_EXT:000001856"},{"id":"T3362","span":{"begin":23,"end":27},"obj":"SO_EXT:0000704"},{"id":"T3363","span":{"begin":52,"end":63},"obj":"SO_EXT:0001080"},{"id":"T3364","span":{"begin":64,"end":68},"obj":"SO_EXT:0000704"},{"id":"T3365","span":{"begin":76,"end":81},"obj":"NCBITaxon:9606"},{"id":"T3366","span":{"begin":82,"end":87},"obj":"PR_EXT:000001856"},{"id":"T3367","span":{"begin":220,"end":240},"obj":"GO_SO_EXT:chromosomal_part_or_position_or_region_or_site"},{"id":"T3368","span":{"begin":252,"end":258},"obj":"NCBITaxon:9606"},{"id":"T3369","span":{"begin":282,"end":290},"obj":"SO_EXT:biological_sequence"},{"id":"T3370","span":{"begin":309,"end":320},"obj":"SO_EXT:0001080"},{"id":"T3371","span":{"begin":321,"end":327},"obj":"SO_EXT:0000417"},{"id":"T3372","span":{"begin":340,"end":346},"obj":"SO_EXT:0000417"},{"id":"T3373","span":{"begin":355,"end":366},"obj":"GO_UBERON_EXT:cellular_component_or_cell_part"},{"id":"T3374","span":{"begin":358,"end":366},"obj":"CL_GO_EXT:cell"},{"id":"T3375","span":{"begin":367,"end":379},"obj":"GO_PATO_EXT:biological_localization_process_or_quality"},{"id":"T3376","span":{"begin":387,"end":392},"obj":"PR_EXT:000001856"},{"id":"T3377","span":{"begin":393,"end":400},"obj":"CHEBI_PR_EXT:protein"},{"id":"T3378","span":{"begin":408,"end":418},"obj":"GO:0005813"},{"id":"T3379","span":{"begin":432,"end":437},"obj":"PR_EXT:000001856"},{"id":"T3380","span":{"begin":610,"end":620},"obj":"NCBITaxon:7742"},{"id":"T3381","span":{"begin":621,"end":627},"obj":"SO_EXT:0001026"},{"id":"T3382","span":{"begin":658,"end":663},"obj":"PR_EXT:000001856"},{"id":"T3383","span":{"begin":664,"end":675},"obj":"SO_EXT:0000855"},{"id":"T3384","span":{"begin":688,"end":693},"obj":"SO_EXT:0000704"},{"id":"T3385","span":{"begin":697,"end":706},"obj":"NCBITaxon:33208"},{"id":"T3386","span":{"begin":749,"end":760},"obj":"SO_EXT:0001080"},{"id":"T3387","span":{"begin":817,"end":822},"obj":"PR_EXT:000001856"},{"id":"T3388","span":{"begin":823,"end":827},"obj":"SO_EXT:0000704"},{"id":"T3389","span":{"begin":835,"end":848},"obj":"NCBITaxon:33511"},{"id":"T3390","span":{"begin":859,"end":863},"obj":"SO_EXT:cDNA"},{"id":"T3391","span":{"begin":871,"end":878},"obj":"SO_EXT:0001026"},{"id":"T3392","span":{"begin":879,"end":887},"obj":"SO_EXT:biological_sequence"},{"id":"T3393","span":{"begin":913,"end":928},"obj":"NCBITaxon:7719"},{"id":"T3394","span":{"begin":933,"end":938},"obj":"PR_EXT:000001856"},{"id":"T3395","span":{"begin":939,"end":943},"obj":"SO_EXT:0000704"},{"id":"T3396","span":{"begin":962,"end":969},"obj":"NCBITaxon:6960"},{"id":"T3397","span":{"begin":973,"end":982},"obj":"NCBITaxon:6231"},{"id":"T3398","span":{"begin":1008,"end":1013},"obj":"PR_EXT:000001856"},{"id":"T3399","span":{"begin":1019,"end":1024},"obj":"SO_EXT:0000704"},{"id":"T3400","span":{"begin":1044,"end":1054},"obj":"NCBITaxon:33317"},{"id":"T3401","span":{"begin":1055,"end":1067},"obj":"NCBITaxon:33511"},{"id":"T3402","span":{"begin":1104,"end":1117},"obj":"NCBITaxon:7586"},{"id":"T3403","span":{"begin":1118,"end":1129},"obj":"NCBITaxon:7712"},{"id":"T3404","span":{"begin":1168,"end":1176},"obj":"SO_EXT:biological_sequence"},{"id":"T3405","span":{"begin":1206,"end":1217},"obj":"SO_EXT:0001080"},{"id":"T3406","span":{"begin":1218,"end":1226},"obj":"CHEBI_PR_EXT:protein"},{"id":"T3407","span":{"begin":1255,"end":1260},"obj":"PR_EXT:000001856"},{"id":"T3408","span":{"begin":1285,"end":1291},"obj":"SO_EXT:0000417"},{"id":"T3409","span":{"begin":1331,"end":1339},"obj":"CHEBI_PR_EXT:protein"},{"id":"T3410","span":{"begin":1347,"end":1358},"obj":"SO_EXT:0001080"},{"id":"T3411","span":{"begin":1425,"end":1429},"obj":"SO_EXT:0000704"}],"text":"Placement of the RHAMM gene in the phylogeny of the coiled coil gene family\nHuman RHAMM has also been proposed to be the missing fourth member of the TACC family [10]. Evidence used in support of this claim included its chromosomal location on 5q32 in humans (discussed below), its sequence similarity in its coiled coil domain to the TACC domain and the subcellular localization of the RHAMM protein in the centrosome. However, if RHAMM were a bona fide TACC family member, then we would predict its evolution would be similar to those of other TACC family members, and fit with the proposed evolution of the vertebrate genome. Thus, we set out to identify RHAMM orthologues and related genes in metazoans, so that a more complete phylogeny of the coiled coil super family could be generated. We identified a single RHAMM gene in all deuterostomes for which cDNA and/or genomic sequence was available, including C. intestinalis. No RHAMM gene was identified in insects or nematodes. This indicates that the RHAMM/TACC genes diverged after the protostome/deuterostome split 833–933 MYA, but prior to the echinodermata/urochordate divergence (\u003e750 MYA). Significantly, sequence and phylogenetic analysis of coiled coil proteins (Fig. 1) clearly shows that RHAMM does not contain a TACC domain and instead forms a distinct family of proteins in the coiled coil superfamily, and is not a direct descendant of the ancestral TACC gene."}
craft-ca-core-dev
{"project":"craft-ca-core-dev","denotations":[{"id":"T3321","span":{"begin":17,"end":22},"obj":"PR:000001856"},{"id":"T3322","span":{"begin":23,"end":27},"obj":"SO:0000704"},{"id":"T3323","span":{"begin":52,"end":63},"obj":"SO:0001080"},{"id":"T3324","span":{"begin":64,"end":68},"obj":"SO:0000704"},{"id":"T3325","span":{"begin":76,"end":81},"obj":"NCBITaxon:9606"},{"id":"T3326","span":{"begin":82,"end":87},"obj":"PR:000001856"},{"id":"T3327","span":{"begin":252,"end":258},"obj":"NCBITaxon:9606"},{"id":"T3328","span":{"begin":309,"end":320},"obj":"SO:0001080"},{"id":"T3329","span":{"begin":321,"end":327},"obj":"SO:0000417"},{"id":"T3330","span":{"begin":340,"end":346},"obj":"SO:0000417"},{"id":"T3331","span":{"begin":387,"end":392},"obj":"PR:000001856"},{"id":"T3332","span":{"begin":408,"end":418},"obj":"GO:0005813"},{"id":"T3333","span":{"begin":432,"end":437},"obj":"PR:000001856"},{"id":"T3334","span":{"begin":610,"end":620},"obj":"NCBITaxon:7742"},{"id":"T3335","span":{"begin":621,"end":627},"obj":"SO:0001026"},{"id":"T3336","span":{"begin":658,"end":663},"obj":"PR:000001856"},{"id":"T3337","span":{"begin":664,"end":675},"obj":"SO:0000855"},{"id":"T3338","span":{"begin":688,"end":693},"obj":"SO:0000704"},{"id":"T3339","span":{"begin":697,"end":706},"obj":"NCBITaxon:33208"},{"id":"T3340","span":{"begin":749,"end":760},"obj":"SO:0001080"},{"id":"T3341","span":{"begin":817,"end":822},"obj":"PR:000001856"},{"id":"T3342","span":{"begin":823,"end":827},"obj":"SO:0000704"},{"id":"T3343","span":{"begin":835,"end":848},"obj":"NCBITaxon:33511"},{"id":"T3344","span":{"begin":871,"end":878},"obj":"SO:0001026"},{"id":"T3345","span":{"begin":913,"end":928},"obj":"NCBITaxon:7719"},{"id":"T3346","span":{"begin":933,"end":938},"obj":"PR:000001856"},{"id":"T3347","span":{"begin":939,"end":943},"obj":"SO:0000704"},{"id":"T3348","span":{"begin":962,"end":969},"obj":"NCBITaxon:6960"},{"id":"T3349","span":{"begin":973,"end":982},"obj":"NCBITaxon:6231"},{"id":"T3350","span":{"begin":1008,"end":1013},"obj":"PR:000001856"},{"id":"T3351","span":{"begin":1019,"end":1024},"obj":"SO:0000704"},{"id":"T3352","span":{"begin":1044,"end":1054},"obj":"NCBITaxon:33317"},{"id":"T3353","span":{"begin":1055,"end":1067},"obj":"NCBITaxon:33511"},{"id":"T3354","span":{"begin":1104,"end":1117},"obj":"NCBITaxon:7586"},{"id":"T3355","span":{"begin":1118,"end":1129},"obj":"NCBITaxon:7712"},{"id":"T3356","span":{"begin":1206,"end":1217},"obj":"SO:0001080"},{"id":"T3357","span":{"begin":1255,"end":1260},"obj":"PR:000001856"},{"id":"T3358","span":{"begin":1285,"end":1291},"obj":"SO:0000417"},{"id":"T3359","span":{"begin":1347,"end":1358},"obj":"SO:0001080"},{"id":"T3360","span":{"begin":1425,"end":1429},"obj":"SO:0000704"}],"text":"Placement of the RHAMM gene in the phylogeny of the coiled coil gene family\nHuman RHAMM has also been proposed to be the missing fourth member of the TACC family [10]. Evidence used in support of this claim included its chromosomal location on 5q32 in humans (discussed below), its sequence similarity in its coiled coil domain to the TACC domain and the subcellular localization of the RHAMM protein in the centrosome. However, if RHAMM were a bona fide TACC family member, then we would predict its evolution would be similar to those of other TACC family members, and fit with the proposed evolution of the vertebrate genome. Thus, we set out to identify RHAMM orthologues and related genes in metazoans, so that a more complete phylogeny of the coiled coil super family could be generated. We identified a single RHAMM gene in all deuterostomes for which cDNA and/or genomic sequence was available, including C. intestinalis. No RHAMM gene was identified in insects or nematodes. This indicates that the RHAMM/TACC genes diverged after the protostome/deuterostome split 833–933 MYA, but prior to the echinodermata/urochordate divergence (\u003e750 MYA). Significantly, sequence and phylogenetic analysis of coiled coil proteins (Fig. 1) clearly shows that RHAMM does not contain a TACC domain and instead forms a distinct family of proteins in the coiled coil superfamily, and is not a direct descendant of the ancestral TACC gene."}
2_test
{"project":"2_test","denotations":[{"id":"15207008-12808028-9665999","span":{"begin":163,"end":165},"obj":"12808028"}],"text":"Placement of the RHAMM gene in the phylogeny of the coiled coil gene family\nHuman RHAMM has also been proposed to be the missing fourth member of the TACC family [10]. Evidence used in support of this claim included its chromosomal location on 5q32 in humans (discussed below), its sequence similarity in its coiled coil domain to the TACC domain and the subcellular localization of the RHAMM protein in the centrosome. However, if RHAMM were a bona fide TACC family member, then we would predict its evolution would be similar to those of other TACC family members, and fit with the proposed evolution of the vertebrate genome. Thus, we set out to identify RHAMM orthologues and related genes in metazoans, so that a more complete phylogeny of the coiled coil super family could be generated. We identified a single RHAMM gene in all deuterostomes for which cDNA and/or genomic sequence was available, including C. intestinalis. No RHAMM gene was identified in insects or nematodes. This indicates that the RHAMM/TACC genes diverged after the protostome/deuterostome split 833–933 MYA, but prior to the echinodermata/urochordate divergence (\u003e750 MYA). Significantly, sequence and phylogenetic analysis of coiled coil proteins (Fig. 1) clearly shows that RHAMM does not contain a TACC domain and instead forms a distinct family of proteins in the coiled coil superfamily, and is not a direct descendant of the ancestral TACC gene."}