RNA id: TCONS_00005989


Basic Information

Item Value
RNA id TCONS_00005989
length 1532
lncRNA type sense_over
GC content 0.41
exon number 1
gene id XLOC_002550
representative False

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

atgatttctccactcaaatgaatggcggcttggacccggaaacagtattacatacgtcaccacttaacaagtggattaaACCAGTAAATGCTGCTGGAGTGTGTGTCAGAGCAGCTCTGGAGATCATCGGCAGATCCTAAATGTTCTGATGGGTTGGTAGTTGAATGTTCTGATGGGTCAGATCCTGAATGTTCTGATTTGGTCTGAGATTgaatgctctgattggtcagtacctggatgttCTGAATGGTCAGATCCTgaatgctctgattggtcagtgcctggatgttctgattggtcagatcctgaatgttctgattggtcagtggcTGAacgttctgattggtcagagccTGGATGTTGATTGGTCAGTGCTTAGTGCTCTGCCCGGTCCGATCCTGAATGTTCTGATTGATCAGTGGttgaatgttctgattggtcaaatccTGGATGTTCTGTTTGCTTACCACTTGATTGTTCTGATCGGTCAGATCCTGATTGGTCAGTTGTTTTTCTGGTAGATCAGTGCCTGGATGTTCTGATTGGCCTGAGCTTAGTCAGTGTTCTGCTTGGTCAGATACTgaatgctctgattggtcagaggcTGGATGTTCTGATTTATCAGTGCCTGATTGGTCAGTGGTTaaatgctctgattggtcagatactGCATGTTCTGATTGCTTAGTGCTTGATAGTTCTGATTGGTTAGTGCTTAGTCAGTGTTCCGATTGCTTAGATCCTGGATGTTCTGATTGATCAGTGCCTGATTGTTTTGCTTGGTCAGTGGTTgaatgctctgattggtcagctactGCATGTTCTGATTGCTTAGTGCTTGATTGTTCTGATTGATCAGTGTCTGATTGTTTTGATTGATCAATCAGAACATTAAACCACtgatcaatcaaatcaatcagacACTGATCATCAATCAGAACATTAAACCACTGACAGTGTCTgattgttctgattggtcagtggtGTAATGTTCTGCTTGGTCAGTGCTTAGTCAAGTCATAACCTGGATATTCTTATTGGTCAGGggaatgttctgattggtcagcgttCTGATTGGCCAGCGGTTTaatcttctgattggtcagctgttAGTCAGTGTTCTAATTGGTCAGTGGTTAATGTTCAGAGCTTTAAAACTTCACAGTCTCAAGTTGAGATGTCATTTCTCTTGCTTTGTTAGTTTTCTtaagaaaacaatgaaaaaaagtgcCAAGTTGCACGTTATTTTTACGTTATTGACAAGTATTACTGATCATATTTCAAATATTCCTCGTTTTACCCATACGCAACAGGATGTGAGCTCTAGCTTGAGTTAACCTTGTATCCGTGGTTCTCGTGATCTCCAATATAAACTAACACtacatttaaaatggcatttatgAAATGCAAATGTTTCACCGTATGCCTTTTCTACATGTATCTCTGTGTGATATCATTTCTGTCATAGCATCACTTATGTGTATATCGCTGATACTAAGGTCTAATAAAGACTTTATCCAAACGTCCTCTAA

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

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00004744 lncRNA downstream 261256 5525393 ~ 5527364 (-) True XLOC_002547
TCONS_00005988 lncRNA downstream 564678 5221915 ~ 5223942 (-) True XLOC_002546
TCONS_00005987 lncRNA downstream 566201 5221915 ~ 5222419 (-) False XLOC_002546
TCONS_00004741 lncRNA downstream 729797 5052862 ~ 5058823 (-) True XLOC_002544
TCONS_00005986 lncRNA downstream 764335 5018558 ~ 5024285 (-) False XLOC_002543
TCONS_00005990 lncRNA upstream 64483 5854634 ~ 5855125 (-) True XLOC_002552
TCONS_00005991 lncRNA upstream 246730 6036881 ~ 6037746 (-) True XLOC_002555
TCONS_00005992 lncRNA upstream 599118 6389269 ~ 6409797 (-) True XLOC_002556
TCONS_00004764 lncRNA upstream 782787 6572938 ~ 6577465 (-) True XLOC_002560
TCONS_00005993 lncRNA upstream 820006 6610157 ~ 6611065 (-) True XLOC_002561
TCONS_00004748 mRNA downstream 104294 5667401 ~ 5684326 (-) True XLOC_002549
TCONS_00004746 mRNA downstream 207133 5536132 ~ 5581487 (-) False XLOC_002548
TCONS_00004745 mRNA downstream 220241 5533843 ~ 5568379 (-) False XLOC_002548
TCONS_00004747 mRNA downstream 220241 5536766 ~ 5568379 (-) True XLOC_002548
TCONS_00004742 mRNA downstream 652832 5092511 ~ 5135788 (-) False XLOC_002545
TCONS_00004750 mRNA upstream 4101 5794252 ~ 5814101 (-) True XLOC_002550
TCONS_00004751 mRNA upstream 33608 5823759 ~ 5847655 (-) False XLOC_002551
TCONS_00004752 mRNA upstream 34137 5824288 ~ 5844915 (-) False XLOC_002551
TCONS_00004753 mRNA upstream 34184 5824335 ~ 5847904 (-) True XLOC_002551
TCONS_00004754 mRNA upstream 62208 5852359 ~ 5854862 (-) False XLOC_002552
TCONS_00004738 other downstream 764335 5020277 ~ 5024285 (-) True XLOC_002543
TCONS_00004737 other downstream 766206 5020186 ~ 5022414 (-) False XLOC_002543
TCONS_00004736 other downstream 768120 5018558 ~ 5020500 (-) False XLOC_002543
TCONS_00004723 other downstream 2019854 3768651 ~ 3768766 (-) True XLOC_002530
TCONS_00004722 other downstream 2281966 3506540 ~ 3506654 (-) True XLOC_002529
TCONS_00004756 other upstream 160312 5950463 ~ 5950578 (-) True XLOC_002554
TCONS_00004759 other upstream 627554 6417705 ~ 6431288 (-) True XLOC_002557
TCONS_00004760 other upstream 682555 6472706 ~ 6472832 (-) True XLOC_002558
TCONS_00004765 other upstream 820924 6611075 ~ 6638235 (-) False XLOC_002562
TCONS_00004766 other upstream 832418 6622569 ~ 6623404 (-) False XLOC_002562

Expression Profile

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