RNA id: TCONS_00043894


Basic Information

Item Value
RNA id TCONS_00043894
length 1689
RNA type mRNA
GC content 0.42
exon number 4
gene id XLOC_022237
representative False

Chromosome Information

Item Value
chromosome id NC_007134.7
NCBI id CM002907.2
chromosome length 46223584
location 16961269 ~ 17004783 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

TGATtagaaggaaaataaaaatagtaccGTGTGTAACATGTTTACATGTATGTCCTGTGAGGAGGAACTTGTGCTGGTGTGAGGCCGTTTGCGCTTCATTTGCAGCAGCATCCGTTTCCTCTGTTTTAAGTTTTCGCGGTAAAGGGGTTGAGGCCATGTGTGCGCAGACACAGAAATGCACTACCAactcttatttatttttgctgagtACGTTACCGCGCGCGcaagtgttttatttaaaataacggTAGGTTAATCTCTCTTCACCCGCCGGCTGACTAAATGACATTAGTTTATCGACGTTTCTATAAGATGACTTTTAAAGGTTATGGAGAATGGTTGTGAATGTAGAGAAACACACGTTTACAAGTTACAAGTGTAATTCAGTAACAGACCAGTCTAGTGGAGTACATCACCTGCTCAGAAACTCTGCTGAATGGTAACATCCAGAAAACCTGTCATTCAAAGAGTTTCAGTTCACAGAGCTTGAAATGCctaGAAGACGTTCATCAAGACTCAGATGTCCaaaacagcaaattaaaaatGGCAAACAAAATTCAAATAATGCATTCACTTGCAATCCAGCCACAATGTGTTTCATCAAAAGGTATGCTTCATCTACCTCAGATTGTGGATCTGTTTCAAAAAATCCAGCATTAGACCAGAAATACTGGGAGGACATTACTGCCATCTGCAGACAGACTCCATACTGCCTTTATCTATACCATGGAGTGGAGATCGAGAATGACAAGAAGGCCAGTGTGCTCTTGTTGGGCTTTTTTGACGAAGATACTGGAAAAAACAAAATCAGACTGCTGGATGTTGTCTATCCAACAAAAGAGTCCACTGAAGACATCTGCAACTACATCTTGGACTTGCTGAGGAAGATCGGAATACCTATATCCAATATGGCCATATTATATTCAGATTTTCCAGATCACGAACATCTTGTAGCTGGTCTACAGTTAATGAAAGCTGAGATTGTGTCTTTATGTGGACTTACAGACCTGACAGGACAAGTGTGTCACAGTGGTGTTGAGAAAATTGAGTTTTCTGACCTGATTCTGAATCTCATCATAGAGATCTACAAACACTTCCCATCTTTCCCAGCAGATCTACAAGCTTTGCTTGAAGATGTTGAAGGATCAGACATTGATAATCTGACATCTCAGTGCTCTCTCTTCTGGAGAATAATTAAGAAAATCTCTTTAGCTTGGTCACATCTTGAGAAGTACTTTGGATCTCTGGATACAGAAGAAGAAGCAGTCTGCCTTCTTCTAGAGGATCCCAAAATAAAGCTCAACGTTCTCTTTCTTACCCACGCTTTGCAGCCGCTTTGTGATTTTCAGGAGATTATCGACCAAGGTGCCAGCGTCTTACAACTGCTCCAAGATGCTTCTAAATTATTGAGGCTTTACACACAGAGTTTCCTCAGACCAAAAGCAGCAGAGTATTTTCACAGGAGAGGAAAGACCTCACTTGTACAGGAGACAGTGGGACATTTACCTAGAGGAGAGGTTGCAGTCGGCGAACAGGCTGCTGATTTTCTCCAGCAGCACTCTGAAGAGTTGTCTGACTACTTGGAGACATTTCACAGATCCATCATCTCCTTCTACACCACTGTTACTGTTAATATTGTCAAACGTCTGCCTCTCCCTGATTCCACCCTGAGAAACTTGTCGTTGGTGT

Function

GO:

id name namespace
GO:0044085 cellular component biogenesis biological_process
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0016070 RNA metabolic process biological_process
GO:0016071 mRNA metabolic process biological_process
GO:0016072 rRNA metabolic process biological_process
GO:0051983 regulation of chromosome segregation biological_process
GO:0051984 positive regulation of chromosome segregation biological_process
GO:0022613 ribonucleoprotein complex biogenesis biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0008152 metabolic process biological_process
GO:0034470 ncRNA processing biological_process
GO:0006364 rRNA processing biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0000375 RNA splicing, via transesterification reactions biological_process
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile biological_process
GO:0000380 alternative mRNA splicing, via spliceosome biological_process
GO:0000381 regulation of alternative mRNA splicing, via spliceosome biological_process
GO:0006396 RNA processing biological_process
GO:0006397 mRNA processing biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0062033 positive regulation of mitotic sister chromatid segregation biological_process
GO:0030490 maturation of SSU-rRNA biological_process
GO:0031323 regulation of cellular metabolic process biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0051785 positive regulation of nuclear division biological_process
GO:0050684 regulation of mRNA processing biological_process
GO:0045840 positive regulation of mitotic nuclear division biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:0006725 cellular aromatic compound metabolic process biological_process
GO:1901360 organic cyclic compound metabolic process biological_process
GO:0010467 gene expression biological_process
GO:0044237 cellular metabolic process biological_process
GO:0010468 regulation of gene expression biological_process
GO:0044238 primary metabolic process biological_process
GO:0042254 ribosome biogenesis biological_process
GO:0042274 ribosomal small subunit biogenesis biological_process
GO:0048024 regulation of mRNA splicing, via spliceosome biological_process
GO:0071704 organic substance metabolic process biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0043170 macromolecule metabolic process biological_process
GO:0033045 regulation of sister chromatid segregation biological_process
GO:0006807 nitrogen compound metabolic process biological_process
GO:1903311 regulation of mRNA metabolic process biological_process
GO:0033047 regulation of mitotic sister chromatid segregation biological_process
GO:0043484 regulation of RNA splicing biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0034660 ncRNA metabolic process biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0008380 RNA splicing biological_process
GO:0071013 catalytic step 2 spliceosome cellular_component
GO:0030684 preribosome cellular_component
GO:0032040 small-subunit processome cellular_component
GO:0044422 obsolete organelle part cellular_component
GO:0044424 obsolete intracellular part cellular_component
GO:1990904 ribonucleoprotein complex cellular_component
GO:0044428 obsolete nuclear part cellular_component
GO:0070013 intracellular organelle lumen cellular_component
GO:0044446 obsolete intracellular organelle part cellular_component
GO:0044451 obsolete nucleoplasm part cellular_component
GO:0044464 obsolete cell part cellular_component
GO:0030532 small nuclear ribonucleoprotein complex cellular_component
GO:0032991 protein-containing complex cellular_component
GO:0005622 intracellular anatomical structure cellular_component
GO:0005623 obsolete cell cellular_component
GO:0005634 nucleus cellular_component
GO:0005654 nucleoplasm cellular_component
GO:0016604 nuclear body cellular_component
GO:0016607 nuclear speck cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005684 U2-type spliceosomal complex cellular_component
GO:0031974 membrane-enclosed lumen cellular_component
GO:0097525 spliceosomal snRNP complex cellular_component
GO:0031981 nuclear lumen cellular_component
GO:0043226 organelle cellular_component
GO:0043227 membrane-bounded organelle cellular_component
GO:0043229 intracellular organelle cellular_component
GO:0043231 intracellular membrane-bounded organelle cellular_component
GO:0043233 organelle lumen cellular_component
GO:0005730 nucleolus cellular_component
GO:0005488 binding molecular_function
GO:0017069 snRNA binding molecular_function
GO:0008187 poly-pyrimidine tract binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0097159 organic cyclic compound binding molecular_function
GO:1901363 heterocyclic compound binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0003727 single-stranded RNA binding molecular_function
GO:0003729 mRNA binding molecular_function
GO:0004386 helicase activity molecular_function
GO:0030623 U5 snRNA binding molecular_function
GO:0036002 pre-mRNA binding molecular_function

KEGG:

id description
ko00230 Purine metabolism
ko00240 Pyrimidine metabolism
ko03020 RNA polymerase
ko03230 Viral genome structure
ko04623 Cytosolic DNA-sensing pathway
ko05164 Influenza A
ko05016 Huntington disease
ko03200 Viral proteins

ZFIN:

id description
ZDB-GENE-050314-2 Predicted to enable DNA (cytosine-5-)-methyltransferase activity; DNA binding activity; and metal ion binding activity. Predicted to act upstream of or within DNA methylation and regulation of gene expression. Predicted to be located in nucleus. Is expressed in several structures, including brain; digestive system; head; musculature system; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in several diseases, including acute myeloid leukemia; autoimmune disease (multiple); carcinoma (multiple); immunodeficiency-centromeric instability-facial anomalies syndrome 1; and thymoma. Orthologous to human DNMT3B (DNA methyltransferase 3 beta) and DNMT3L (DNA methyltransferase 3 like).

Ensembl:

ensembl_id ENSDART00000125472

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00043892 lncRNA downstream 16371 16961269 ~ 16962540 (-) False XLOC_022237
TCONS_00044724 lncRNA downstream 125964 16850836 ~ 16852947 (-) True XLOC_022235
TCONS_00043885 lncRNA downstream 241759 16735911 ~ 16737152 (-) True XLOC_022232
TCONS_00043884 lncRNA downstream 244982 16730519 ~ 16733929 (-) False XLOC_022232
TCONS_00044723 lncRNA downstream 269673 16693578 ~ 16709238 (-) False XLOC_022231
TCONS_00043902 lncRNA upstream 372254 17354153 ~ 17355702 (-) True XLOC_022241
TCONS_00043904 lncRNA upstream 446072 17427971 ~ 17429764 (-) True XLOC_022242
TCONS_00043907 lncRNA upstream 450699 17432598 ~ 17439938 (-) False XLOC_022243
TCONS_00043914 lncRNA upstream 465024 17446923 ~ 17450731 (-) True XLOC_022243
TCONS_00043919 lncRNA upstream 676095 17657994 ~ 17663102 (-) False XLOC_022247
TCONS_00043888 mRNA downstream 17939 16956185 ~ 16960972 (-) True XLOC_022236
TCONS_00043887 mRNA downstream 135262 16840572 ~ 16843649 (-) True XLOC_022234
TCONS_00043883 mRNA downstream 241750 16722998 ~ 16737161 (-) False XLOC_022232
TCONS_00043882 mRNA downstream 244902 16719743 ~ 16734009 (-) False XLOC_022232
TCONS_00043879 mRNA downstream 286599 16688420 ~ 16692312 (-) True XLOC_022230
TCONS_00043896 mRNA upstream 30 16981929 ~ 17003533 (-) False XLOC_022237
TCONS_00043897 mRNA upstream 1464 16983363 ~ 17004783 (-) False XLOC_022237
TCONS_00043899 mRNA upstream 29555 17011454 ~ 17101360 (-) True XLOC_022238
TCONS_00043903 mRNA upstream 445939 17427838 ~ 17429775 (-) False XLOC_022242
TCONS_00043905 mRNA upstream 449446 17431345 ~ 17450805 (-) False XLOC_022243
TCONS_00043889 other downstream 14806 16961269 ~ 16964105 (-) False XLOC_022237
TCONS_00043886 other downstream 232488 16744782 ~ 16746423 (-) True XLOC_022233
TCONS_00043880 other downstream 269680 16696410 ~ 16709231 (-) False XLOC_022231
TCONS_00043881 other downstream 269747 16696519 ~ 16709164 (-) True XLOC_022231
TCONS_00043875 other downstream 416750 16561233 ~ 16562161 (-) True XLOC_022227
TCONS_00043898 other upstream 1878 16983777 ~ 16984594 (-) True XLOC_022237
TCONS_00043900 other upstream 62395 17044294 ~ 17046384 (-) True XLOC_022239
TCONS_00043901 other upstream 194205 17176104 ~ 17176218 (-) True XLOC_022240
TCONS_00043921 other upstream 700919 17682818 ~ 17682932 (-) True XLOC_022248
TCONS_00043939 other upstream 1081274 18063173 ~ 18063299 (-) True XLOC_022255

Expression Profile

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