RNA id: TCONS_00003000


Basic Information

Item Value
RNA id TCONS_00003000
length 725
lncRNA type sense_over
GC content 0.61
exon number 5
gene id XLOC_000002
representative False

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 18716 ~ 23389 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

gcagcagcagcagcagcagcagaagatGATCATCGACCGAGTTTCTGACGGGTTTTCGGGTCTGCTGGACCGGGACGCGGATCTGATAAGTCCGGTGCAGCTGTGGGGCTTCCCCGGCTGCAGTTCCCCCACAGAGCCGCTGCTGTCCCCGGGAGAGCCCAGCTCCGACTCCGAGCACAGCTGGAGCGACGCCAGCGtGGAGGCGGAGGGCACACGCAGGAGCCGCTATCAGGGTGTGCGCGTCAAGAACACGGTGAAGGAACTGATCATGCGCAGAAAACACCtacacacacaggtgcagcagcagcagttcgCCGTCGATGACGAGTGCGCAGtgctGCAGAGCAGGAAGAGGACAGCAGagagtgtgtgtttctctgctgTGAAGCGCGCGCGAGCCACTGACGGATACACACCGatGGAGTGTGTGTCCAGTGACTGTGATCTGCTGGAGGATCTCGGGGTTTTTCTGGCTCCGCCTCTCTCCGTGGGCTCAGTGATGGAGAGTGTGTGTGCAGACGCGCCACCGCTTTACATGCAGAACACACTCCCCGCTGTGCAGAACACACTCCCCGCTGTGCAGAACACACTCCCCGCTGTGCAGAACACACTCCCCGCCGCGCCGCCAGTTTCCTTCTTCCAATGGCAGATCCAGCAGGAGGATGAGAAACTGTCTGCGTTGAGCCCTGCGGAGCTGATGAGCCGAGATGAGGACGGAGACacgt

Function

GO:

id name namespace
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway biological_process
GO:0001704 formation of primary germ layer biological_process
GO:0048729 tissue morphogenesis biological_process
GO:0010604 positive regulation of macromolecule metabolic process 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:0035239 tube morphogenesis biological_process
GO:0022603 regulation of anatomical structure morphogenesis biological_process
GO:0007492 endoderm development biological_process
GO:0007498 mesoderm development biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0002009 morphogenesis of an epithelium biological_process
GO:0018130 heterocycle biosynthetic process biological_process
GO:0006351 transcription, DNA-templated biological_process
GO:0065007 biological regulation biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0051173 positive regulation of nitrogen compound metabolic process biological_process
GO:0036342 post-anal tail morphogenesis biological_process
GO:0048785 hatching gland development biological_process
GO:0048513 animal organ development biological_process
GO:0003401 axis elongation biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0090036 regulation of protein kinase C signaling 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:0045165 cell fate commitment biological_process
GO:0009888 tissue development biological_process
GO:0009889 regulation of biosynthetic process biological_process
GO:0009893 positive regulation of metabolic 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:0030509 BMP signaling pathway 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:0044237 cellular metabolic process biological_process
GO:0010468 regulation of gene expression biological_process
GO:0044238 primary metabolic process biological_process
GO:0048869 cellular developmental process biological_process
GO:0010470 regulation of gastrulation biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0044260 cellular macromolecule metabolic process biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0070121 Kupffer's vesicle development 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:0043170 macromolecule metabolic process biological_process
GO:0003002 regionalization biological_process
GO:0007389 pattern specification process biological_process
GO:0050789 regulation of biological process biological_process
GO:0050794 regulation of cellular process 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:0019438 aromatic compound biosynthetic process biological_process
GO:0010556 regulation of macromolecule biosynthetic process biological_process
GO:0060026 convergent extension biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0060028 convergent extension involved in axis elongation biological_process
GO:0060029 convergent extension involved in organogenesis 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:0071772 response to BMP biological_process
GO:0071773 cellular response to BMP stimulus 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:0001702 gastrulation with mouth forming second biological_process
GO:0005634 nucleus cellular_component
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:0097159 organic cyclic compound 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:1901363 heterocyclic compound binding 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
ko05202 Transcriptional misregulation in cancer
ko03000 Transcription factors
ko03110 Chaperones and folding catalysts

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00000004 lncRNA upstream 3653 14167 ~ 15063 (+) False XLOC_000001
TCONS_00000013 lncRNA downstream 7483 27814 ~ 31905 (+) False XLOC_000004
TCONS_00003001 lncRNA downstream 7483 27814 ~ 32353 (+) False XLOC_000004
TCONS_00000014 lncRNA downstream 7518 27849 ~ 31321 (+) False XLOC_000004
TCONS_00000015 lncRNA downstream 11456 31787 ~ 32353 (+) True XLOC_000004
TCONS_00000017 lncRNA downstream 16396 36727 ~ 38446 (+) True XLOC_000005
TCONS_00000001 mRNA upstream 2343 11822 ~ 16373 (+) False XLOC_000001
TCONS_00000011 mRNA downstream 5254 25585 ~ 27255 (+) True XLOC_000003
TCONS_00000012 mRNA downstream 7359 27690 ~ 34330 (+) False XLOC_000004
TCONS_00000016 mRNA downstream 16221 36552 ~ 39191 (+) False XLOC_000005
TCONS_00000018 mRNA downstream 89467 109798 ~ 119146 (+) True XLOC_000006
TCONS_00000019 mRNA downstream 99629 119960 ~ 125246 (+) True XLOC_000007
TCONS_00000003 other upstream 5459 12129 ~ 13257 (+) False XLOC_000001
TCONS_00000036 other downstream 239709 260040 ~ 293894 (+) False XLOC_000017
TCONS_00000047 other downstream 493682 514013 ~ 515322 (+) True XLOC_000021
TCONS_00000052 other downstream 517258 537589 ~ 546217 (+) False XLOC_000023
TCONS_00000053 other downstream 556113 576444 ~ 576521 (+) True XLOC_000024
TCONS_00000060 other downstream 1198360 1218691 ~ 1218805 (+) True XLOC_000029

Expression Profile

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