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ONTOLOGY REPORT - ANNOTATIONS


Term:ciliary plasm
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Accession:GO:0097014 term browser browse the term
Definition:All of the contents of a cilium, excluding the plasma membrane surrounding the cilium.
Comment:Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm".
Synonyms:exact_synonym: cilium plasm
 narrow_synonym: microtubule-based flagellar matrix;   microtubule-based flagellum matrix
 related_synonym: cilial cytoplasm;   ciliary cytoplasm;   cilium cytoplasm;   microtubule-based flagellar cytoplasm;   microtubule-based flagellum cytoplasm


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ciliary plasm term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dync2i1 dynein 2 intermediate chain 1 JBrowse link 6 144,069,077 144,124,975 RGD:13792537
G Dync2i2 dynein 2 intermediate chain 2 JBrowse link 3 8,599,251 8,615,329 RGD:13792537
G Nek4 NIMA-related kinase 4 JBrowse link 16 7,035,002 7,080,272 RGD:13204813
A axonemal microtubule term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cfap206 cilia and flagella associated protein 206 JBrowse link 5 50,148,685 50,193,580 RGD:1600115
axonemal basal plate term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ift88 intraflagellar transport 88 JBrowse link 15 37,690,417 37,786,855 RGD:1624291
G Wdpcp WD repeat containing planar cell polarity effector JBrowse link 14 106,393,959 106,759,511 RGD:1624291
RGD:1600115
axonemal central apparatus term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G LOC102550841 uncharacterized LOC102550841 JBrowse link 9 76,913,521 77,007,087 RGD:13792537
G Spag16 sperm associated antigen 16 JBrowse link 9 77,027,626 77,833,476 RGD:1624291
RGD:13792537
G Spag17 sperm associated antigen 17 JBrowse link 2 202,159,659 202,452,361 RGD:1624291
RGD:13792537
G Spag6l sperm associated antigen 6-like JBrowse link 11 88,424,493 88,517,910 RGD:1624291
axonemal central pair projection term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Hydin Hydin, axonemal central pair apparatus protein JBrowse link 19 41,036,507 41,379,634 RGD:1624291
axonemal dynein complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ccdc65 coiled-coil domain containing 65 JBrowse link 7 140,383,395 140,397,186 RGD:1600115
G Dnah1 dynein, axonemal, heavy chain 1 JBrowse link 16 7,345,131 7,407,009 RGD:1600115
RGD:13792537
G Dnah12 dynein, axonemal, heavy chain 12 JBrowse link 16 2,377,218 2,534,130 RGD:13792537
G Dnah5 dynein, axonemal, heavy chain 5 JBrowse link 2
2
80,947,730
81,159,060
81,143,997
81,337,560
RGD:1624291
G Dnah7 dynein, axonemal, heavy chain 7 JBrowse link 9
9
60,070,087
59,564,253
60,330,121
59,595,347
RGD:13792537
G Dnai2 dynein, axonemal, intermediate chain 2 JBrowse link 10 103,266,343 103,301,521 RGD:1624291
G Dnai4 dynein axonemal intermediate chain 4 JBrowse link 5 122,551,370 122,642,161 RGD:13792537
RGD:1624291
RGD:1600115
G Dnhd1 dynein heavy chain domain 1 JBrowse link 1 170,473,792 170,570,220 RGD:13792537
G Drc1 dynein regulatory complex subunit 1 JBrowse link 6 27,425,237 27,460,038 RGD:1600115
axonemal microtubule term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Arfgef2 ADP ribosylation factor guanine nucleotide exchange factor 2 JBrowse link 3 163,570,435 163,656,612 RGD:1304338
G Cep162 centrosomal protein 162 JBrowse link 8 94,863,282 94,921,917 RGD:1624291
RGD:1600115
G Rpgrip1l Rpgrip1-like JBrowse link 19 17,115,266 17,208,055 RGD:11537356
G Saxo1 stabilizer of axonemal microtubules 1 JBrowse link 5 104,771,081 104,921,001 RGD:1624291
RGD:13792537
G Saxo2 stabilizer of axonemal microtubules 2 JBrowse link 1 144,586,260 144,601,358 RGD:13792537
G Saxol1 stabilizer of axonemal microtubules like 1 JBrowse link X 29,520,263 29,522,420 RGD:1600115
RGD:13792537
G Ttc30a1 tetratricopeptide repeat domain 30A1 JBrowse link 3 62,800,932 62,803,373 RGD:13792537
G Ttc30b tetratricopeptide repeat domain 30B JBrowse link 3 62,758,754 62,761,325 RGD:13792537
RGD:1600115
axoneme term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07063281.1 RGD:13792537
G Ak8 adenylate kinase 8 JBrowse link 3 7,279,429 7,394,509 RGD:1624291
G Akap14 A-kinase anchoring protein 14 JBrowse link X 123,773,430 123,788,898 RGD:1624291
G Ambra1 autophagy and beclin 1 regulator 1 JBrowse link 3 80,634,470 80,830,068 RGD:1624291
G Arl13b ADP-ribosylation factor like GTPase 13B JBrowse link 7 1,122,567 1,188,209 RGD:1624291
G Arl3 ADP ribosylation factor like GTPase 3 JBrowse link 1 266,287,015 266,333,099 RGD:1600115
RGD:1624291
G Arl6 ADP-ribosylation factor like GTPase 6 JBrowse link 11 42,858,476 42,884,324 RGD:13792537
G Armc4 armadillo repeat containing 4 JBrowse link 17 60,283,926 60,474,289 RGD:1624291
G Atg14 autophagy related 14 JBrowse link 15 24,343,418 24,374,776 RGD:1624291
RGD:1600115
G Atg16l1 autophagy related 16-like 1 JBrowse link 9 94,879,876 94,915,231 RGD:1624291
G Atg5 autophagy related 5 JBrowse link 20 49,301,783 49,393,147 RGD:1624291
RGD:1600115
G Atg7 autophagy related 7 JBrowse link 4 146,570,113 146,777,093 RGD:1624291
RGD:1600115
G Bbs1 Bardet-Biedl syndrome 1 JBrowse link 1 220,146,084 220,165,545 RGD:13792537
G Bbs5 Bardet-Biedl syndrome 5 JBrowse link 3 55,886,695 55,907,717 RGD:1624291
G Bbs7 Bardet-Biedl syndrome 7 JBrowse link 2 123,283,402 123,322,991 RGD:1624291
RGD:13792537
G Ccdc114 coiled-coil domain containing 114 JBrowse link 1 101,904,042 101,932,999 RGD:1624291
RGD:13792537
G Ccdc151 coiled-coil domain containing 151 JBrowse link 8 23,000,912 23,014,707 RGD:1624291
G Ccdc39 coiled-coil domain containing 39 JBrowse link 2 120,278,605 120,367,829 RGD:1600115
RGD:13792537
RGD:1624291
G Ccdc40 coiled-coil domain containing 40 JBrowse link 10 108,055,270 108,393,408 RGD:1624291
G Ccdc63 coiled-coil domain containing 63 JBrowse link 12 39,905,120 39,950,719 RGD:13792537
G Ccdc65 coiled-coil domain containing 65 JBrowse link 7 140,383,395 140,397,186 RGD:13792537
G Ccsap centriole, cilia and spindle-associated protein JBrowse link 19 56,615,326 56,634,031 RGD:1624291
RGD:13792537
G Cenpf centromere protein F JBrowse link 13 108,132,499 108,178,609 RGD:1624291
G Cfap36 cilia and flagella associated protein 36 JBrowse link 14 113,618,954 113,644,874 RGD:13792537
G Cfap43 cilia and flagella associated protein 43 JBrowse link 1 267,511,359 267,598,642 RGD:13792537
RGD:1624291
G Cfap70 cilia and flagella associated protein 70 JBrowse link 15 4,285,049 4,350,707 RGD:1624291
G Cluap1 clusterin associated protein 1 JBrowse link 10 11,847,058 11,878,792 RGD:1624291
G Ctsh cathepsin H JBrowse link 8 97,439,155 97,458,293 RGD:5686399
G Cys1 cystin 1 JBrowse link 6 43,844,937 43,862,131 RGD:1624291
G Dcdc2 doublecortin domain containing 2 JBrowse link 17 41,838,201 42,031,265 RGD:1600115
RGD:13792537
RGD:1624291
G Dcx doublecortin JBrowse link X 115,098,675 115,175,515 RGD:13792537
G Dnaaf1 dynein, axonemal, assembly factor 1 JBrowse link 19 52,217,427 52,245,930 RGD:1600115
RGD:13792537
RGD:1624291
G Dnah1 dynein, axonemal, heavy chain 1 JBrowse link 16 7,345,131 7,407,009 RGD:1624291
RGD:1600115
G Dnah11 dynein, axonemal, heavy chain 11 JBrowse link 6 145,784,893 146,099,212 RGD:1624291
RGD:13792537
G Dnah17 dynein, axonemal, heavy chain 17 JBrowse link 10 107,028,115 107,161,288 RGD:1624291
RGD:13792537
G Dnah2 dynein, axonemal, heavy chain 2 JBrowse link 10 56,029,022 56,154,602 RGD:1624291
RGD:13792537
G Dnah5 dynein, axonemal, heavy chain 5 JBrowse link 2
2
80,947,730
81,159,060
81,143,997
81,337,560
RGD:1600115
RGD:13792537
RGD:1624291
G Dnah8 dynein, axonemal, heavy chain 8 JBrowse link 20 9,301,317 9,560,805 RGD:1624291
G Dnah9 dynein, axonemal, heavy chain 9 JBrowse link 10 52,351,226 52,711,289 RGD:1624291
RGD:13792537
G Dnai2 dynein, axonemal, intermediate chain 2 JBrowse link 10 103,266,343 103,301,521 RGD:1624291
G Dnai4 dynein axonemal intermediate chain 4 JBrowse link 5 122,551,370 122,642,161 RGD:1600115
RGD:1624291
G Dnajb13 DnaJ heat shock protein family (Hsp40) member B13 JBrowse link 1 165,515,718 165,530,163 RGD:1624291
G Dnali1 dynein, axonemal, light intermediate chain 1 JBrowse link 5 143,053,365 143,062,203 RGD:13792537
RGD:1624291
RGD:1600115
G Drc1 dynein regulatory complex subunit 1 JBrowse link 6 27,425,237 27,460,038 RGD:1600115
RGD:13792537
G Drc3 dynein regulatory complex subunit 3 JBrowse link 10 46,712,021 46,762,276 RGD:1624291
G Dync2h1 dynein cytoplasmic 2 heavy chain 1 JBrowse link 8 5,217,054 5,436,969 RGD:1624291
RGD:13792537
RGD:1600115
G Dync2i2 dynein 2 intermediate chain 2 JBrowse link 3 8,599,251 8,615,329 RGD:1624291
G Dync2li1 dynein cytoplasmic 2 light intermediate chain 1 JBrowse link 6 7,900,962 7,933,795 RGD:1624291
RGD:13792537
G Dzip1l DAZ interacting zinc finger protein 1-like JBrowse link 8 107,875,659 107,916,298 RGD:1624291
G Efhc1 EF-hand domain containing 1 JBrowse link 9 27,068,505 27,107,713 RGD:1624291
RGD:13792537
G Efhc2 EF-hand domain containing 2 JBrowse link X 5,825,551 6,026,398 RGD:13792537
G Gabarap GABA type A receptor-associated protein JBrowse link 10 56,601,288 56,604,223 RGD:1624291
RGD:1600115
G Gas8 growth arrest specific 8 JBrowse link 19 56,316,367 56,335,873 RGD:1600115
RGD:1624291
G Gli1 GLI family zinc finger 1 JBrowse link 7 70,620,794 70,633,171 RGD:1624291
G Gli2 GLI family zinc finger 2 JBrowse link 13 34,829,021 35,049,172 RGD:1624291
G Gli3 GLI family zinc finger 3 JBrowse link 17 52,294,942 52,569,036 RGD:1624291
G Gnat3 G protein subunit alpha transducin 3 JBrowse link 4 13,827,764 13,878,126 RGD:2302145
G Ift140 intraflagellar transport 140 JBrowse link 10 14,373,668 14,461,509 RGD:1624291
RGD:13792537
G Ift172 intraflagellar transport 172 JBrowse link 6 26,390,686 26,485,459 RGD:13792537
G Ift57 intraflagellar transport 57 JBrowse link 11 53,664,638 53,731,779 RGD:1624291
G Ift88 intraflagellar transport 88 JBrowse link 15 37,690,417 37,786,855 RGD:1624291
G Inpp5e inositol polyphosphate-5-phosphatase E JBrowse link 3 3,843,307 3,856,154 RGD:1624291
RGD:1600115
G Kif17 kinesin family member 17 JBrowse link 5 156,628,409 156,665,752 RGD:1624291
G Kif19 kinesin family member 19 JBrowse link 10 103,308,392 103,334,466 RGD:1600115
G Kif3a kinesin family member 3a JBrowse link 10 38,918,705 38,953,958 RGD:1581597
G Kifap3 kinesin-associated protein 3 JBrowse link 13 82,072,497 82,217,256 RGD:1624291
RGD:13792537
G Lca5 lebercilin LCA5 JBrowse link 8 90,926,309 90,984,271 RGD:1624291
RGD:13792537
G Lca5l lebercilin LCA5 like JBrowse link 11 36,512,823 36,546,806 RGD:13792537
G LOC103689994 radial spoke head protein 4 homolog A JBrowse link 20 33,945,770 33,962,077 RGD:13792537
G LOC103691261 sperm flagellar protein 1-like JBrowse link 1 212,309,940 212,317,411 RGD:13792537
G Mak male germ cell-associated kinase JBrowse link 17 21,531,651 21,567,742 RGD:1624291
G Map1lc3b microtubule-associated protein 1 light chain 3 beta JBrowse link 19 53,635,449 53,643,970 RGD:1624291
G Map4 microtubule-associated protein 4 JBrowse link 8 118,013,584 118,159,934 RGD:1624291
G Mapk15 mitogen-activated protein kinase 15 JBrowse link 7 117,041,287 117,061,799 RGD:1624291
G Mapt microtubule-associated protein tau JBrowse link 10 92,289,002 92,386,517 RGD:1624291
G Mns1 meiosis-specific nuclear structural 1 JBrowse link 8 79,054,240 79,075,119 RGD:1624291
G Pik3c3 phosphatidylinositol 3-kinase, catalytic subunit type 3 JBrowse link 18 22,964,121 23,047,896 RGD:1600115
G Pik3r4 phosphoinositide-3-kinase, regulatory subunit 4 JBrowse link 8 114,300,248 114,350,686 RGD:1624291
RGD:1600115
G Prkaca protein kinase cAMP-activated catalytic subunit alpha JBrowse link 19 25,095,089 25,118,869 RGD:1624291
RGD:1600115
G Prkar1a protein kinase cAMP-dependent type I regulatory subunit alpha JBrowse link 10 97,940,705 97,959,199 RGD:1624291
G Prkar2a protein kinase cAMP-dependent type II regulatory subunit alpha JBrowse link 8 117,486,085 117,548,768 RGD:1600115
RGD:1624291
G Rp1 RP1, axonemal microtubule associated JBrowse link 5 15,005,028 15,060,508 RGD:13792537
RGD:1624291
G Rp1l1 RP1 like 1 JBrowse link 15 47,344,380 47,384,461 RGD:1624291
RGD:13792537
G Rpgrip1 RPGR interacting protein 1 JBrowse link 15 28,521,287 28,575,046 RGD:1624291
G Rpgrip1l Rpgrip1-like JBrowse link 19 17,115,266 17,208,055 RGD:1624291
G Rsph4a radial spoke head component 4A JBrowse link 20 32,450,701 32,467,362 RGD:1624291
RGD:13792537
G Rsph6a radial spoke head 6 homolog A JBrowse link 1 79,959,555 79,979,217 RGD:1624291
RGD:13792537
G Rsph9 radial spoke head component 9 JBrowse link 9 17,224,589 17,245,093 RGD:1624291
RGD:13792537
G Septin2 septin 2 JBrowse link 9 100,624,876 100,658,053 RGD:1624291
G Septin7 septin 7 JBrowse link 8 26,412,910 26,476,615 RGD:1624291
RGD:1600115
G Septin9 septin 9 JBrowse link 10 106,208,308 106,340,747 RGD:1624291
G Septin9 septin 9 RGD:1600115
G Spag16 sperm associated antigen 16 JBrowse link 9 77,027,626 77,833,476 RGD:1624291
G Spata4 spermatogenesis associated 4 JBrowse link 16 39,961,160 39,970,530 RGD:13792537
G Spata7 spermatogenesis associated 7 JBrowse link 6 122,603,248 122,648,718 RGD:1600115
RGD:13792537
RGD:1624291
G Spef1 sperm flagellar 1 JBrowse link 3 123,712,907 123,720,787 RGD:13792537
G Tctex1d2 Tctex1 domain containing 2 JBrowse link 11 71,593,302 71,601,662 RGD:1624291
G Tctex1d4 Tctex1 domain containing 4 JBrowse link 5 135,995,128 135,997,807 RGD:1624291
G Tmem67 transmembrane protein 67 JBrowse link 5 25,666,138 25,721,056 RGD:11535084
G Traf3ip1 TRAF3 interacting protein 1 JBrowse link 9 98,621,499 98,658,223 RGD:1624291
RGD:13792537
G Ttc25 tetratricopeptide repeat domain 25 JBrowse link 10 88,459,490 88,488,237 RGD:1624291
G Ttll10 tubulin tyrosine ligase like 10 JBrowse link 5 173,471,020 173,517,783 RGD:1624291
RGD:1600115
G Ttll3 tubulin tyrosine ligase like 3 JBrowse link 4 145,341,059 145,366,614 RGD:1624291
G Ttll8 tubulin tyrosine ligase like 8 JBrowse link 7 129,906,998 129,948,578 RGD:1624291
G Tubb4a tubulin, beta 4A class IVa JBrowse link 9 9,961,020 9,968,420 RGD:1624291
G Tulp3 TUB like protein 3 JBrowse link 4 161,636,084 161,677,807 RGD:1624291
G Wdpcp WD repeat containing planar cell polarity effector JBrowse link 14 106,393,959 106,759,511 RGD:1600115
G Wdr11 WD repeat domain 11 JBrowse link 1 202,770,810 202,816,336 RGD:1624291
G Wdr35 WD repeat domain 35 JBrowse link 6 34,094,291 34,152,048 RGD:1624291
RGD:13792537
RGD:1600115
distal portion of axoneme term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnah9 dynein, axonemal, heavy chain 9 JBrowse link 10 52,351,226 52,711,289 RGD:1624291
inner dynein arm term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnah1 dynein, axonemal, heavy chain 1 JBrowse link 16 7,345,131 7,407,009 RGD:1624291
RGD:13792537
G Dnah12 dynein, axonemal, heavy chain 12 JBrowse link 16 2,377,218 2,534,130 RGD:13792537
G Dnah7 dynein, axonemal, heavy chain 7 JBrowse link 9
9
60,070,087
59,564,253
60,330,121
59,595,347
RGD:1624291
RGD:13792537
RGD:1600115
G Dnai3 dynein axonemal intermediate chain 3 JBrowse link 2 251,912,432 251,970,699 RGD:13792537
G Dnhd1 dynein heavy chain domain 1 JBrowse link 1 170,473,792 170,570,220 RGD:13792537
outer dynein arm term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ccdc103 coiled-coil domain containing 103 JBrowse link 10 90,984,213 90,987,829 RGD:1600115
G Ccdc114 coiled-coil domain containing 114 JBrowse link 1 101,904,042 101,932,999 RGD:1624291
RGD:1600115
G Cfap70 cilia and flagella associated protein 70 JBrowse link 15 4,285,049 4,350,707 RGD:1624291
G Dnah17 dynein, axonemal, heavy chain 17 JBrowse link 10 107,028,115 107,161,288 RGD:1624291
G Dnah5 dynein, axonemal, heavy chain 5 JBrowse link 2
2
80,947,730
81,159,060
81,143,997
81,337,560
RGD:1624291
G Dnah8 dynein, axonemal, heavy chain 8 JBrowse link 20 9,301,317 9,560,805 RGD:13792537
G Dnai1 dynein, axonemal, intermediate chain 1 JBrowse link 5 57,947,796 58,017,985 RGD:1624291
RGD:13792537
G Dnai2 dynein, axonemal, intermediate chain 2 JBrowse link 10 103,266,343 103,301,521 RGD:1624291
RGD:13792537
G Nme8 NME/NM23 family member 8 JBrowse link 17 47,300,932 47,368,543 RGD:1624291
RGD:1600115
outer dynein arm docking complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ttc25 tetratricopeptide repeat domain 25 JBrowse link 10 88,459,490 88,488,237 RGD:1624291
proximal portion of axoneme term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dnah11 dynein, axonemal, heavy chain 11 JBrowse link 6 145,784,893 146,099,212 RGD:1624291
radial spoke term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cfap206 cilia and flagella associated protein 206 JBrowse link 5 50,148,685 50,193,580 RGD:1600115
G Rsph6a radial spoke head 6 homolog A JBrowse link 1 79,959,555 79,979,217 RGD:1600115
G Rsph9 radial spoke head component 9 JBrowse link 9 17,224,589 17,245,093 RGD:1600115
radial spoke head term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Rsph4a radial spoke head component 4A JBrowse link 20 32,450,701 32,467,362 RGD:1624291

Term paths to the root
Path 1
Term Annotations click to browse term
  cellular_component 20300
    cellular anatomical entity 19956
      organelle 12977
        cilium 681
          ciliary plasm 130
            axoneme + 128
Path 2
Term Annotations click to browse term
  cellular_component 20300
    intracellular 14243
      cytoplasm 11099
        cytoplasmic region 290
          plasma membrane bounded cell projection cytoplasm 236
            ciliary plasm 130
              axoneme + 128
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.