RNA id: TCONS_00004750


Basic Information

Item Value
RNA id TCONS_00004750
length 2601
RNA type mRNA
GC content 0.47
exon number 15
gene id XLOC_002550
representative True

Chromosome Information

Item Value
chromosome id NC_007121.7
NCBI id CM002894.2
chromosome length 45420867
location 5788620 ~ 5821584 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATGGACACTTCACATCATTGGCTGTTGGTCTTGATGCTCTTGCATTATGCAAAAGGTTCCAACAGTAGCTGTGTATTAAAAATTCTTCCAGACTCCAAGACTAAGATTCCTGTTGAGTTGGAAAGAAACTTCACAGCGACATGCCACCTCCAGGGTGGATCTGAATTTACCTCAAATGACATCAAATGGTCTTTTAGCAACAAAGAAACTACAGACATTTTATCAAAGACATTTTATCACAAAATAAATGAAACCTCCGTCAGTGTTACAGTTAACCTCAGCAAAAACATGGGTCATATGTTGATGTGTGAAGCCTCCAGAGAGTCCTTAACATACATGGGAAAATGTGCCTACGGAATCTACCTTGATGCAGGATACCCTCCGATGAAACCAAAGAATCTGACATGCATTGCTTTGCAAAGGAAGAAGGATATTTCTCCTGACCTAAATTGTTATTGGGAACCAGGATTGAGAGACCCACTGCTTGCCACCAATTATACTCTTTATGCCCAAGTAGGACAAGATTTATATAACAGCACCTGTAAACAGAGTCTTGCAAGAAGTTGCACCGTCAACCTGAGCACTTATCCTGTTCATATGACTTTGAAAGTCTGGGTTGAAGTGAAAAATTCACTGGGGTCAGAACGGTCAGACGAACACGAGTACGATTCCTTGAGTCTTGTGAAACCAAATCCACCAAATGTCGAAGTTAAAGTTGAAGAGGACTTCCCTACATCTTTTGTGGTTAAATGGGAGTATGACATTGAAGACACAACTATGCGATTCTCCAGTGCCATTAGATACTGCCAAGTAGGGTCAAGTGATTGgaaaaaggtgCCTGAGAACTACACCAATGTGCACATTACGTCGTATCGACTGCAGTCCCTAGAGCCTTACACTGAGTATGTGGTACAGATGCGATCCATCGGAGAGCACTACACCATCTGGAGTGAATGGAGCTCCAATGTTACAGTTCGCACTCCAGAAGCCAGGGAATTCCCACTGCCATTTTTGAAGTGCGTTGCACTTTGTGAAGTGGTCAATGCAAGTTTATATGAACAGACCCTTGACCTGTCAATTTTGACTAAGCCTCCTGTGAAAGCTAATGGAAAAATGTGTAACTATTCCCTGATCATCAGTCAAGATAACCAGGCTTTTGAAAGTCACGTTATAAAAGCTGATCAGCTCAACCAGAGGTATTCACTGGAAGTGCCACCAGAAGAAAATGCCAGTATTGAAATAACTGCATTCAATTCAGCCGGAGGGTCTCCCAAAACTATTTTGTTCATTCCAAGATCAAATGACGAGTTTCTTGGCGTGGCGAGCATGAGGTGGTGGGTTCATGATGGAAAGCTTCATGTGGAATGGGGTCCTTTGAAGCAGCATCCTCCTCATGGCATTCATATCTCAGAATATCTGCTGGAGTGGGTGAATGAAAAAGATGTTCAGCCTCAGTGGCAGAGGGTTCCTAAAAATGTCAACACCACCATACTGAACGGTAATTTAGCCAAATACAAGCAGTACAACATATCAGTCTATCCAATCTACAAGTTCTATTATGATGGTCGATGGCATTTCCAAGCAGGAACACCAGTAACCAAGCCAGCCTACGTTCAGCAAGGAGCACCAGAGAAAGGCCCTACTGTCACAGATACCATTTCCAAGAAAAATAGTGTTACACTGATATGGGAGGAAATTCCACTGGACCACCGGTATGGATTCATCCAAAACTACACCATATTCTACAGGACCGGCAACGCTGAGTGGCAATCTGTGCTAGTGGCCGCTAACATCCACTCGTATGTATTGACTGATCTGGTCAGTGAACGCGACTATGTGGTTCACATCATGGCCTCGACGGAAGCTGGCTCCAAAAACGGCACCGattttaatttcaaaacaatGAAGTTCGCCGATGGAGAGGTGGAGATGATTGTAGTGCTGGTGTGCCTCGGCTTCCTGTTCCTGAGCGTCTTCACCATAATGCTCTGCCTTCGCAAGAGAGAAGTGATTAAGAAGCTGTTATGGCCGCAAGTCCCGGATCCGTCTGACAGCTCTATTGCCCACTGGTCACCTGATTTCCCTGTAAAGACCGAAATGCCCAAGGAAGACGTCAGCGTGGTGGAAGTGGACGTGTTTGACGGCAAGTCTTTGTGCGAAGAAGATAAAGTTGTTCTGCCGCTAAAGAAGGACAAGTACCTCTCCGAGGAGCACAGCAGCGGTATTGGAGGCTCGTCCTGCATGTCTTCGCCCCGCCACAGTGTTTCCGACAGCGATGAGGGCGACTCGGGCCAGACCACGGCCAGCACCGTCCAGTACTCGTCAGTGGTGGCCAGCGGATACAAGGGCCAAACCCCAAACCATCAGCCTCCAACGTTCGCCCGCTCCGAGTCCACACAACCGCTGCTGGACTGCGAGGAGCATCCAGAGAATCATCCCGGCGAGAGGAACTCTTACTTTAGACGGGGCCGAGAGCTGGAGCCGCAGAGTATCGATGAGCCTGTTTTCAGCGCGGTGCAGGAGGAAGAAGCATCTCCCGTTGTGGATGATGCGCCGGCGTTAAGTTACATGCCGCAGCAGAGCGGGTATCGACCGCAGTAA

Function

GO:

id name namespace
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0016070 RNA metabolic process biological_process
GO:0016071 mRNA metabolic process biological_process
GO:0008152 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:0009060 aerobic respiration biological_process
GO:0006403 RNA localization biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0050657 nucleic acid transport biological_process
GO:0050658 RNA transport biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0051236 establishment of RNA localization biological_process
GO:0050684 regulation of mRNA processing 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:0051276 chromosome organization biological_process
GO:0051028 mRNA transport biological_process
GO:0048024 regulation of mRNA splicing, via spliceosome biological_process
GO:0071704 organic substance metabolic process biological_process
GO:0006807 nitrogen compound metabolic process biological_process
GO:1903311 regulation of mRNA metabolic process biological_process
GO:0043484 regulation of RNA splicing biological_process
GO:0045292 mRNA cis splicing, via spliceosome biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0008380 RNA splicing biological_process
GO:0071010 prespliceosome cellular_component
GO:0071013 catalytic step 2 spliceosome cellular_component
GO:0071565 nBAF complex 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:0070603 SWI/SNF superfamily-type complex cellular_component
GO:0030532 small nuclear ribonucleoprotein complex cellular_component
GO:0032991 protein-containing complex cellular_component
GO:1990204 oxidoreductase complex cellular_component
GO:0005622 intracellular anatomical structure cellular_component
GO:0005623 obsolete cell cellular_component
GO:0005634 nucleus cellular_component
GO:0120114 Sm-like protein family complex cellular_component
GO:0005654 nucleoplasm cellular_component
GO:0016604 nuclear body cellular_component
GO:0016607 nuclear speck cellular_component
GO:1902494 catalytic complex cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005684 U2-type spliceosomal complex cellular_component
GO:0005685 U1 snRNP cellular_component
GO:0005686 U2 snRNP 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:1904949 ATPase complex cellular_component
GO:0071004 U2-type prespliceosome cellular_component
GO:0005488 binding molecular_function
GO:0019829 ATPase-coupled cation transmembrane transporter activity molecular_function
GO:0022853 active ion transmembrane transporter activity molecular_function
GO:0044769 ATPase activity, coupled to transmembrane movement of ions, rotational mechanism 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:0042625 ATPase-coupled ion transmembrane transporter activity molecular_function

KEGG:

id description
ko00230 Purine metabolism
ko00240 Pyrimidine metabolism
ko03020 RNA polymerase
ko03230 Viral genome structure
ko05164 Influenza A
ko03200 Viral proteins

ZFIN:

id description
ZDB-GENE-080104-6 Predicted to enable cytokine binding activity and cytokine receptor activity. Acts upstream of or within positive regulation of axon regeneration. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be part of receptor complex. Predicted to be active in external side of plasma membrane. Is expressed in several structures, including epidermis; immune system; liver; muscle; and sensory system. Human ortholog(s) of this gene implicated in arteriosclerosis; hyper IgE recurrent infection syndrome 4; hyperandrogenism; and primary localized cutaneous amyloidosis 2. Orthologous to several human genes including IL6ST (interleukin 6 cytokine family signal transducer).

Ensembl:

ensembl_id ENSDART00000161903

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00005989 lncRNA downstream 4101 5788620 ~ 5790151 (-) False XLOC_002550
TCONS_00004744 lncRNA downstream 266888 5525393 ~ 5527364 (-) True XLOC_002547
TCONS_00005988 lncRNA downstream 570310 5221915 ~ 5223942 (-) True XLOC_002546
TCONS_00005987 lncRNA downstream 571833 5221915 ~ 5222419 (-) False XLOC_002546
TCONS_00004741 lncRNA downstream 735429 5052862 ~ 5058823 (-) True XLOC_002544
TCONS_00005990 lncRNA upstream 40533 5854634 ~ 5855125 (-) True XLOC_002552
TCONS_00005991 lncRNA upstream 222780 6036881 ~ 6037746 (-) True XLOC_002555
TCONS_00005992 lncRNA upstream 575168 6389269 ~ 6409797 (-) True XLOC_002556
TCONS_00004764 lncRNA upstream 758837 6572938 ~ 6577465 (-) True XLOC_002560
TCONS_00005993 lncRNA upstream 796056 6610157 ~ 6611065 (-) True XLOC_002561
TCONS_00004748 mRNA downstream 109926 5667401 ~ 5684326 (-) True XLOC_002549
TCONS_00004746 mRNA downstream 212765 5536132 ~ 5581487 (-) False XLOC_002548
TCONS_00004745 mRNA downstream 225873 5533843 ~ 5568379 (-) False XLOC_002548
TCONS_00004747 mRNA downstream 225873 5536766 ~ 5568379 (-) True XLOC_002548
TCONS_00004743 mRNA downstream 658464 5094123 ~ 5135788 (-) True XLOC_002545
TCONS_00004751 mRNA upstream 9658 5823759 ~ 5847655 (-) False XLOC_002551
TCONS_00004752 mRNA upstream 10187 5824288 ~ 5844915 (-) False XLOC_002551
TCONS_00004753 mRNA upstream 10234 5824335 ~ 5847904 (-) True XLOC_002551
TCONS_00004754 mRNA upstream 38258 5852359 ~ 5854862 (-) False XLOC_002552
TCONS_00004755 mRNA upstream 41158 5855259 ~ 5857548 (-) True XLOC_002553
TCONS_00004738 other downstream 769967 5020277 ~ 5024285 (-) True XLOC_002543
TCONS_00004737 other downstream 771838 5020186 ~ 5022414 (-) False XLOC_002543
TCONS_00004736 other downstream 773752 5018558 ~ 5020500 (-) False XLOC_002543
TCONS_00004723 other downstream 2025486 3768651 ~ 3768766 (-) True XLOC_002530
TCONS_00004722 other downstream 2287598 3506540 ~ 3506654 (-) True XLOC_002529
TCONS_00004756 other upstream 136362 5950463 ~ 5950578 (-) True XLOC_002554
TCONS_00004759 other upstream 603604 6417705 ~ 6431288 (-) True XLOC_002557
TCONS_00004760 other upstream 658605 6472706 ~ 6472832 (-) True XLOC_002558
TCONS_00004765 other upstream 796974 6611075 ~ 6638235 (-) False XLOC_002562
TCONS_00004766 other upstream 808468 6622569 ~ 6623404 (-) False XLOC_002562

Expression Profile

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