RNA id: TCONS_00043898


Basic Information

Item Value
RNA id TCONS_00043898
length 527
RNA type processed_transcript
GC content 0.39
exon number 4
gene id XLOC_022237
representative True

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

ggtaaaaaaagcTTAATCTATTGGCCTTTGCCTTTTTatataagtcacttctgataccaaatgatcaactaaaagtcaagatattagttgttgttcctaaaatttggataggtgacaagacttttgtcaggtagtggatATTGgcatagttttaaaaatgtatttgtttgcttttttatttgtgtggTTTTTGTTTTTAGTGTAACCCTGTGCTTGTTGATGCCGTGAAAGTGAGTCCAGCTCACAGAGCAAGATACTTCTGGGGGAACATACCTGGCATGAACAGACCAATCATAGCATCTCAGAATGATAAACTCTGTCTTCAAGAATGTCTGGAGCCTGGCCGCACTGCAAAGTATGAAAAAGTTCGCACTATCACTACACGGCAAAACTCCCTGAAGCAGGGCACCAATGATGCACATTTCCCCGTCACCATGAATGGTAAAGATGACCACATATGGATCACAGAATTGGAgaaAATATTTGGATTTCCGAAGCATTACACTGATGTGAAAAGCATGGGTCGT

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-990712-11 Predicted to enable DNA (cytosine-5-)-methyltransferase activity; DNA binding activity; and metal ion binding activity. Acts upstream of or within several processes, including exocrine pancreas development; eye morphogenesis; and pharyngeal system development. Predicted to be located in nucleus. Is expressed in several structures, including brain; digestive system; eye; 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).

Ensembl:

ensembl_id ENSDART00000127151

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00043892 lncRNA downstream 21237 16961269 ~ 16962540 (-) False XLOC_022237
TCONS_00044724 lncRNA downstream 130830 16850836 ~ 16852947 (-) True XLOC_022235
TCONS_00043885 lncRNA downstream 246625 16735911 ~ 16737152 (-) True XLOC_022232
TCONS_00043884 lncRNA downstream 249848 16730519 ~ 16733929 (-) False XLOC_022232
TCONS_00044979 lncRNA downstream 274647 16696124 ~ 16709130 (-) False XLOC_022231
TCONS_00043902 lncRNA upstream 369559 17354153 ~ 17355702 (-) True XLOC_022241
TCONS_00043904 lncRNA upstream 443377 17427971 ~ 17429764 (-) True XLOC_022242
TCONS_00043907 lncRNA upstream 448004 17432598 ~ 17439938 (-) False XLOC_022243
TCONS_00043914 lncRNA upstream 462329 17446923 ~ 17450731 (-) True XLOC_022243
TCONS_00043919 lncRNA upstream 673400 17657994 ~ 17663102 (-) False XLOC_022247
TCONS_00043895 mRNA downstream 1792 16979462 ~ 16981985 (-) False XLOC_022237
TCONS_00043890 mRNA downstream 1797 16961269 ~ 16981980 (-) False XLOC_022237
TCONS_00043894 mRNA downstream 1878 16978911 ~ 16981899 (-) False XLOC_022237
TCONS_00043891 mRNA downstream 3564 16961578 ~ 16980213 (-) False XLOC_022237
TCONS_00043888 mRNA downstream 22805 16956185 ~ 16960972 (-) True XLOC_022236
TCONS_00043899 mRNA upstream 26860 17011454 ~ 17101360 (-) True XLOC_022238
TCONS_00043903 mRNA upstream 443244 17427838 ~ 17429775 (-) False XLOC_022242
TCONS_00043905 mRNA upstream 446751 17431345 ~ 17450805 (-) False XLOC_022243
TCONS_00043906 mRNA upstream 446754 17431348 ~ 17450811 (-) False XLOC_022243
TCONS_00043908 mRNA upstream 448135 17432729 ~ 17450761 (-) False XLOC_022243
TCONS_00043893 other downstream 4862 16977930 ~ 16978915 (-) False XLOC_022237
TCONS_00043889 other downstream 19672 16961269 ~ 16964105 (-) False XLOC_022237
TCONS_00043886 other downstream 237354 16744782 ~ 16746423 (-) True XLOC_022233
TCONS_00043880 other downstream 274546 16696410 ~ 16709231 (-) False XLOC_022231
TCONS_00043881 other downstream 274613 16696519 ~ 16709164 (-) True XLOC_022231
TCONS_00043900 other upstream 59700 17044294 ~ 17046384 (-) True XLOC_022239
TCONS_00043901 other upstream 191510 17176104 ~ 17176218 (-) True XLOC_022240
TCONS_00043921 other upstream 698224 17682818 ~ 17682932 (-) True XLOC_022248
TCONS_00043939 other upstream 1078579 18063173 ~ 18063299 (-) True XLOC_022255
TCONS_00043945 other upstream 1397862 18382456 ~ 18382551 (-) True XLOC_022260

Expression Profile

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