RNA id: TCONS_00007109


Basic Information

Item Value
RNA id TCONS_00007109
length 3633
RNA type mRNA
GC content 0.41
exon number 5
gene id XLOC_003656
representative True

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 39928828 ~ 39956925 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CAACCGTCACTAATAAACACAAGTCTTCTTTGTAAAATCAATTTAGAAAGGAGCACGTATCGAGTCTAACTGCTGGAGGATTTCACCGCTGAGATTCCTGCAGTGACCACATGATCTGAGGGCAAACGGTGCCTTCCACGTCTGGGTGTggaatGTCCGCTCCAGGTGCAGATGCCTCTGGATCTTCAGGGAGTAACCGCAGGCTGCAGCAGACACAGGCTCAGGTCGATGAGGTGGTGGATATCATGAGAGTGAATGTTGATAAAGTCCTGGAACGAGACCAGAAGCTGTCAGAGCTGGATGATCGTGCTGATGCCCTGCAGGCCGGAGCGTCTCAGTTTGAGACCAGCGCCGCCAAACTCAAGAGGAAATTCTGGTGGAAGAACGTCAAGATGTGGGCCATTTTGATAGCTGTGGTTGtgatcatcattatcatcattgtcAtCTGGTCGCAGTCATAAAGTGGCACAGAGTCTGGTTGTGATCGGAGGAAAAGATCAGGATATGAAGGAGTATTCACTTCAGAAAgaagagtgaatgaatgaacaaccgGTTGCTCTTCCAATAAGTTCTAACCTGCTGATTTTCAAATGCATATTTTGTAAACTATCTTCAatgggttttttttcttttaggttttgtttttaatgactAGATTTGAATATGTTATGAATTCAATTCCAAAATACATCAAACACACTCCTTTTGTGCTCAGCAAGTGAGACGTGTTACATAATTActcagaaacacacaaacaacaggtTGCCATCATAATATATCGACCAAAACCCATCTAAACTCTTGTTTTGAAAGCCATCTGAGTTCCTCGTGGACTGTATTTTATCAGACTGCTGAAATCAGACACTCTTTCTGTGTCAACATGATATGAGAGCCTTTCCTGAACAACCACAGACGTGCCATTAGATATACCAGCAGATAAACTCCACTGCCAACCTCTAATGAAACACCTGCacagaaatattatatataagatTGAGATATTATTGAATTTTGAAGTGATCACTCGCTAGTAATTTAACTGCCTTATATCTATTGCCTTGTGTAGAATTAATTTGCTTAGAAATAGCTTCGCTTAACAAGATCTCAGTAGTATTGAATTTTTGGGGGGCTTTCTTCACCTCTTGCTCACGGTGCCAAAACTTTTTTATGCTATGTTTGAGCTTATTTTGTATGTGTCTCTTTGTATGTCTCACATGTGTATAAATTGTAAACAAGTGCAATTCTATACTGTGGCCTTACAAACTGAATTGCCCCAAGTTGGCTTAATAAACCCAGGATTTAACATCCTTTTGTACTCACCTTAATTTTGTTTCTTgccatgttttattattatattctacaAAATGTGTGTTcacaaatttattcattcattttcgtccGTTTTTCCGTGGCCGGGTCACGGggacagcagtcttaggagacAATCCCAGACTTCActctccagacacttcctccagctcctccgggggatcCTGAGgctttcccaggccagccgagatatatagtccctccagcgtgtactgtaagggtgtcacgatcctccaaatcctcgattcgattacatttttgattctaaaggcacgattcgattcgattatgaataattaattaattaatgaccaattaattatttgtagcctaccgtttaaaccacctgacctgcatggtctttgttttacccataaacaaatcatacagtaaatgaataaaggcaagatacacacataattaccacctgtcaatcactttttctgcgggactcgtgaatgggcagtgatctgtgtcgttataatggcgtcggtaaaaaagacgcacaacaggaaccagccaacagtatctgaggtgttcgctaaaatgactaagtacaagtgagtgaaagcttgaagcagtcctctgactgcctggacctgctgtctcgagcgcatggctgtgtgtgcgtctgtgtctgtgtggtcatgtgatgtgcattcagaggtagagaggaaggagggctgctcagaaacgctacacgccactgtggatgtcaaatcgttgtcgttctaaaatgccatttaaaaacaaagacagtgtaaacagggcctgagtgtgtacttttcgcgagcggatttgcaacgggggtggACGGAGGAACGCGATGccagtgttgtctatcggacgaaccgtacgtaatacgtaaatagcagagcttgcaaaactgtggggtttttttgtcgacaacacgaacgttgtcaacataactcactggaaatccaaaatgcttacacaccggcgacttcattgaaagaggagagggtttaagttctgtcgacgggtctcctgcttttgcagtttaacaagcacttccacaagcctgtttttttcccgcttggcaagccaagctgacgtgacatgggggtgtggcagcatcgacgattctattttttaattcgataatcgaaattgagcataaatttcgatcgatttcgattaaaaatctaaatcgtgaaACCCCTAGTGTACTGGGTCTTTTCCGAGGCCTCCTCcctgtgggacatgcctggaacacctcaattggtaggcatccaggaggcatccgaaacagatgcccgagccacctcagttgacttctcttgatgtggaggagcagcggctcaacTTCGAgttcctcccgggtgacagatcTCCTCACCTTAAGGGTGCGCCCTTCCGCCATGCAAACAAAACTCATTCTGgtcacttgtatccgagatcttgtctttGACCCAAACCTCATGACCATAGTTGAGAGTAGGAGCGTAGATTAaccggtaaattgagagctttgcctttcggctcagctcctccTTTACCACAACgcaccggtacatcgaccgcatcactgctgcaccaatccccatcaatctcacgttccatcgtTCTCTCACTCGTGAACTCAGGTGTTCTCAAGTGTTCACAAATGAGAAATATAAATGTGCAACCAAAAATGaactttaaaatgtcttaatgcTAAAACAGATGCAGAAACAACATTTAACAGTTTAAGTTTCTATCCACCTTGTTTTTTAGGTAACTTGCTGTTAATGTTTTATAGTAGTATTCTGATTTTTGGTCTGATACTTCTATATCATTAGCAGTAATAAAGGCATCttgtgaaattaaattattttagaaaattattttaatgtaatatcaTAAAAACATTGTTTAGCTCAAGTGATATTGTTTgtaattaaccctttaactgccccaccaaataaaaaaacatttgaattgcattacttAACTCCTCATGTCGCTaattaacacactcaatgcatttttttcccacACATCccttaatttctaaaatatcagcctctaccaaatgcttgatatgtcagtttatggttgaagtaccagaattaatacatatactattaaaaatctgaaaatatcaaGTGCTAgtgttaaaaaaatcattttgagtTTCCAAAACACACAGTTAGGTCGATAAATATTTGGACAAACAATTGTAAAATTTTTGGCTctttacaccaacacaatggaaaTGAAACGAACAAGACGTGCtgtaactgcagactgtcagcctTAATTTAaaggtatttacatccaaatcaggtgaacgctgtagga

Function

GO:

id name namespace
GO:0035493 SNARE complex assembly biological_process
GO:0006906 vesicle fusion biological_process
GO:0016192 vesicle-mediated transport biological_process
GO:0005886 plasma membrane cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0031201 SNARE complex cellular_component
GO:0005484 SNAP receptor activity molecular_function
GO:0017075 syntaxin-1 binding molecular_function
GO:0019905 syntaxin binding molecular_function

KEGG:

id description
ko04130 SNARE interactions in vesicular transport
ko04145 Phagosome
ko04131 Membrane trafficking

ZFIN:

id description
ZDB-GENE-040625-45 Predicted to enable SNAP receptor activity and syntaxin-1 binding activity. Predicted to be involved in SNARE complex assembly. Predicted to act upstream of or within vesicle-mediated transport. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be part of SNARE complex. Predicted to be active in plasma membrane. Orthologous to human VAMP3 (vesicle associated membrane protein 3).

Ensembl:

ensembl_id ENSDART00000187653

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00008419 lncRNA upstream 12615 39909576 ~ 39922539 (+) True XLOC_003655
TCONS_00008672 lncRNA upstream 120202 39576541 ~ 39814952 (+) False XLOC_003655
TCONS_00008418 lncRNA upstream 455887 39373712 ~ 39479267 (+) False XLOC_003654
TCONS_00008671 lncRNA upstream 558067 39373720 ~ 39377087 (+) True XLOC_003654
TCONS_00008417 lncRNA upstream 644520 39287369 ~ 39290634 (+) True XLOC_003653
TCONS_00007112 lncRNA downstream 12379 39969304 ~ 39977128 (+) False XLOC_003657
TCONS_00007113 lncRNA downstream 37072 39993997 ~ 39998798 (+) True XLOC_003657
TCONS_00008673 lncRNA downstream 154556 40111481 ~ 40116646 (+) True XLOC_003659
TCONS_00008674 lncRNA downstream 263130 40220055 ~ 40434080 (+) True XLOC_003662
TCONS_00007123 lncRNA downstream 640638 40597563 ~ 40603087 (+) True XLOC_003664
TCONS_00007106 mRNA upstream 8282 39672874 ~ 39926872 (+) False XLOC_003655
TCONS_00007105 mRNA upstream 8282 39672874 ~ 39926872 (+) False XLOC_003655
TCONS_00007103 mRNA upstream 786956 39135050 ~ 39148198 (+) False XLOC_003649
TCONS_00007102 mRNA upstream 793073 39120332 ~ 39142081 (+) False XLOC_003649
TCONS_00007110 mRNA downstream 2114 39959039 ~ 40021080 (+) False XLOC_003657
TCONS_00007111 mRNA downstream 12123 39969048 ~ 40014177 (+) False XLOC_003657
TCONS_00007114 mRNA downstream 75865 40032790 ~ 40072301 (+) False XLOC_003658
TCONS_00007115 mRNA downstream 86644 40043569 ~ 40072068 (+) True XLOC_003658
TCONS_00007116 mRNA downstream 191256 40148181 ~ 40168378 (+) True XLOC_003660
TCONS_00007097 other upstream 1131416 38803611 ~ 38803738 (+) True XLOC_003642
TCONS_00007094 other upstream 1346588 38588451 ~ 38588566 (+) True XLOC_003640
TCONS_00007079 other upstream 2284190 37638982 ~ 37650964 (+) False XLOC_003630
TCONS_00007127 other downstream 692546 40649471 ~ 40655871 (+) False XLOC_003667
TCONS_00007131 other downstream 932255 40889180 ~ 40889294 (+) True XLOC_003670
TCONS_00007137 other downstream 1153744 41110669 ~ 41157928 (+) False XLOC_003675
TCONS_00007139 other downstream 1178684 41135609 ~ 41157926 (+) True XLOC_003675
TCONS_00007149 other downstream 1508182 41465107 ~ 41465236 (+) True XLOC_003680

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
striped catfish (Pangasianodon hypophthalmus) TU368157 False 2248 TUCP 0.39 6 NC_047614.1 19768990 ~ 19783913 (+)
bowfin (Amia calva) AMCG00002094 False 1793 mRNA 0.49 6 CM030136.1 3113477 ~ 3128440 (-)