RNA id: TCONS_00018972


Basic Information

Item Value
RNA id TCONS_00018972
length 1495
lncRNA type antisense_over
GC content 0.33
exon number 2
gene id XLOC_008539
representative True

Chromosome Information

Item Value
chromosome id NC_007126.7
NCBI id CM002899.2
chromosome length 48040578
location 25568937 ~ 25570599 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

tagattatatacatttttatttccacagtatttatttctttttaatcttttggcagaaacaaacagatatgtaagtgtttttgtaattgcaactttaaaataacagACAGAATTAATGACATAGCACAATGAACTAATACCATACTTCAGAAGTACCTCAATAAGTGAATGCGACCTTACCTTTTCCAACAAACTCCACCATGATGTCCGCCTGATGGGAATACGACCTCAAGAATGTGAGAGGACTGGCTTTGGCCCAGACATCCAGAGCCGAAGAGATCAGATCATCCACTGCATTCACTGACGCCACATCGAGGAGTCCTCATGACAGCGAGAGTGTCTGCGTTCAGGGTTCCTGTCCCGTTCAAACCAAAAAAACCCTGCATATTCTTCAGTTTAGAAGAGAAAGAGGGACGACTTCTTCTTTTGCGGCCTGCAGAATCTGCTTGAAAACTATAGAATTGCTGCAAGTATTTCTGTAGAAACACAGTAAATAGCAATTAAAATGTAAAGCCTGACTTTGCATGTGTATGATCTAAAGTAAAAAAagttgcatttgtgtatttttattatattatgtcagTAGAATGTATGTTTTTGATATATGTAAGTAAACAATAATTATGATATAATTATTGTGAAACTGAGAAAATGTGTCGGGTCAGAGGGAAAGATAGAAGAACAAATGATTACACCTAAACATGAAGTTAAATATTTTGGTTGCATCTTAAATAGCAATTTGACAGGTAAGAAGATAGCTGGTATAGTCCATTCAAAAATTTGttctaaaatgacattttttttgcaaGACAGGGAGAGCTCTTAGATACCcaaacttaaatatatttaaaaaatattgcctAGTGCATTAGTGCAGCATACTTCTACTATTGATACAGCCTTTTGGTACAAAAGGTAGTTctaaaaagtgaaaaataaattgCAGTCCAAAATAAGTTGTGTAGAATTGTCATGAAAGTACCTCCACTGACACATTTACATGAAAAACATTCtagtaaaagtatttttattcaagTCGAAAAAACGTTTTTGAAATTAGTGATGATGTTAAAGATTTTACAGAAAATGGTAGCAAAATATTTTCTTGATGATCATGTTTAAGTTATTGAGGTACACTGCATTCTTCAAGAGCAAGTAGCAGGTATTATTCTTGAAGATTTAAGAGTGAAATGGGTAAAAATACTTTTTAGGTACACTAGCTTTGTTGCTTTGTATAAATTGCCTATAAGCGTTTTAAAGAGATTCAATTTGTGTGTTTTAGAAGGGAAATTAAAAAATGGTTGTTTTATGGTTGAAATTGAAGATCTTGTTGACGAGTTGCTGAGCTGACGATGTTTGCACTCCTTTTATGATTTGCTTGTTCGATTTGCTCGTTTTTAGGATTTTCAAGGACCCCAATGAAAATAAGACTGGCATTTTTGTGTATTTCATCCTCAACAGTTTTTAAACTTTATGTGAATCAGTGTAATTGGac

Function

GO:

id name namespace
GO:0001704 formation of primary germ layer biological_process
GO:0048729 tissue morphogenesis biological_process
GO:0001706 endoderm formation biological_process
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0001711 endodermal cell fate commitment biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0001714 endodermal cell fate specification biological_process
GO:0016070 RNA metabolic process biological_process
GO:0007492 endoderm development biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0018130 heterocycle biosynthetic process biological_process
GO:0006351 transcription, DNA-templated biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0060896 neural plate pattern specification biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0060897 neural plate regionalization biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0048785 hatching gland development biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0003154 BMP signaling pathway involved in determination of left/right symmetry biological_process
GO:0035295 tube development biological_process
GO:0009058 biosynthetic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:1901576 organic substance biosynthetic process biological_process
GO:0009887 animal organ morphogenesis biological_process
GO:0009888 tissue development biological_process
GO:0009889 regulation of biosynthetic process biological_process
GO:0097659 nucleic acid-templated transcription biological_process
GO:0031323 regulation of cellular metabolic process biological_process
GO:0060429 epithelium development biological_process
GO:0035050 embryonic heart tube development biological_process
GO:0031326 regulation of cellular biosynthetic process biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0048568 embryonic organ development biological_process
GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway biological_process
GO:1903224 regulation of endodermal cell differentiation biological_process
GO:0010453 regulation of cell fate commitment 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:1903506 regulation of nucleic acid-templated transcription biological_process
GO:1901362 organic cyclic compound biosynthetic process biological_process
GO:0048598 embryonic morphogenesis biological_process
GO:0010467 gene expression biological_process
GO:0010468 regulation of gene expression biological_process
GO:0010470 regulation of gastrulation biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0048332 mesoderm morphogenesis biological_process
GO:0007369 gastrulation biological_process
GO:1900094 regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0003002 regionalization biological_process
GO:0007389 pattern specification process biological_process
GO:0061311 cell surface receptor signaling pathway involved in heart development biological_process
GO:0061312 BMP signaling pathway involved in heart development biological_process
GO:0060795 cell fate commitment involved in formation of primary germ layer biological_process
GO:2001141 regulation of RNA biosynthetic process biological_process
GO:0032774 RNA biosynthetic process biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0019438 aromatic compound biosynthetic process biological_process
GO:0010556 regulation of macromolecule biosynthetic process biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0003303 BMP signaling pathway involved in heart jogging biological_process
GO:0034654 nucleobase-containing compound biosynthetic process biological_process
GO:0035987 endodermal cell differentiation biological_process
GO:2000112 regulation of cellular macromolecule biosynthetic process biological_process
GO:0042659 regulation of cell fate specification biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0072045 convergent extension involved in nephron morphogenesis biological_process
GO:0042663 regulation of endodermal cell fate specification biological_process
GO:1901213 regulation of transcription from RNA polymerase II promoter involved in heart development biological_process
GO:0009790 embryo development biological_process
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003690 double-stranded DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000976 transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:0140110 transcription regulator activity molecular_function
GO:0001067 regulatory region nucleic acid binding molecular_function
GO:1990837 sequence-specific double-stranded DNA binding molecular_function

KEGG:

id description
ko03230 Viral genome structure
ko05164 Influenza A
ko03200 Viral proteins

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00017066 lncRNA upstream 39512 25528309 ~ 25529425 (+) True XLOC_008538
TCONS_00018971 lncRNA upstream 169363 25395901 ~ 25399574 (+) True XLOC_008533
TCONS_00018968 lncRNA upstream 191443 25370567 ~ 25377494 (+) False XLOC_008532
TCONS_00018969 lncRNA upstream 191443 25370731 ~ 25377494 (+) False XLOC_008532
TCONS_00018970 lncRNA upstream 191443 25370791 ~ 25377494 (+) True XLOC_008532
TCONS_00018973 lncRNA downstream 325866 25896465 ~ 25902650 (+) False XLOC_008543
TCONS_00018974 lncRNA downstream 1105386 26675985 ~ 26680699 (+) True XLOC_008549
TCONS_00017087 lncRNA downstream 1726077 27296676 ~ 27300833 (+) True XLOC_008552
TCONS_00018778 lncRNA downstream 1761258 27331857 ~ 27332639 (+) True XLOC_008553
TCONS_00018975 lncRNA downstream 2139731 27710330 ~ 27712387 (+) False XLOC_008558
TCONS_00017065 mRNA upstream 26345 25528290 ~ 25542592 (+) False XLOC_008538
TCONS_00017064 mRNA upstream 69419 25489406 ~ 25499518 (+) True XLOC_008537
TCONS_00017062 mRNA upstream 82927 25452092 ~ 25486010 (+) True XLOC_008535
TCONS_00017060 mRNA upstream 120311 25438714 ~ 25448626 (+) False XLOC_008534
TCONS_00017061 mRNA upstream 125912 25439106 ~ 25443025 (+) True XLOC_008534
TCONS_00017067 mRNA downstream 64727 25635326 ~ 25656327 (+) False XLOC_008540
TCONS_00017068 mRNA downstream 64727 25635326 ~ 25656331 (+) False XLOC_008540
TCONS_00017069 mRNA downstream 64728 25635327 ~ 25656327 (+) False XLOC_008540
TCONS_00017072 mRNA downstream 110445 25681044 ~ 25690267 (+) False XLOC_008542
TCONS_00017073 mRNA downstream 112470 25683069 ~ 25688468 (+) True XLOC_008542
TCONS_00017063 other upstream 99092 25469729 ~ 25469845 (+) True XLOC_008536
TCONS_00017050 other upstream 606685 24962136 ~ 24962252 (+) True XLOC_008523
TCONS_00017035 other upstream 885647 24676913 ~ 24683290 (+) False XLOC_008517
TCONS_00017027 other upstream 999875 24563768 ~ 24569062 (+) False XLOC_008513
TCONS_00016993 other upstream 2118251 23446189 ~ 23450686 (+) True XLOC_008495
TCONS_00017070 other downstream 64742 25635341 ~ 25656331 (+) True XLOC_008540
TCONS_00017071 other downstream 96988 25667587 ~ 25667701 (+) True XLOC_008541
TCONS_00017074 other downstream 326847 25897446 ~ 25897539 (+) False XLOC_008543
TCONS_00017075 other downstream 327116 25897715 ~ 25897799 (+) True XLOC_008543
TCONS_00017076 other downstream 535716 26106315 ~ 26106433 (+) True XLOC_008544

Expression Profile

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