RNA id: TCONS_00042787


Basic Information

Item Value
RNA id TCONS_00042787
length 2828
lncRNA type lincRNA
GC content 0.37
exon number 3
gene id XLOC_021544
representative False

Chromosome Information

Item Value
chromosome id NC_007134.7
NCBI id CM002907.2
chromosome length 46223584
location 15478745 ~ 15483879 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATGAAGGCCAAACAGCCTCCTTTCAAAAGAGCACGTCAGGACAAAGAACCTTCCGCTGCTGTGGCAAGTGACTATGATGCTGATTCCAGTGCTTCAACAGTCATTCTGTCATCGCCTTCAAGTTCAAGCACCCCACGGCAAGAAAATGACAGCATTGATGAAGCATCTGATGGTCCTGACAACAGCCTTGACAGCCAGAAAACCCAGGCAAGACATTACAGGACCCTACAAGAAATGTACAAAGCAAAGAAGCCAAATAaagctgctgtaacccatctatTAGACCTGGAGTTCCAGTCCAGAAGAAGTTTCATTGACTCAAATGTATTGAAGGAGCAAGACAAACCCACAAATATTTTGCAAGCGTACCCCTGCTTCAAAGAATTGGACCATGCAATGGATGAACTACGAAGAATCATTGAGCCAAACAACTCCAAATACATTTCTGAGGTGAAGGACAGGTGGGAGACCTTCTACTCCAAGGTTCAGTTTTATGGAGTGATGAAAAAAGTCATGAAGCCTCCAAGGACATTAAATGgaggtaaaactttaatttaatttgaatctgTATAGATCAAGGGTTCTCAACTCTGGTCCTTAAGGTCCAGTATAActccaatcctaattaaacaaacctgagcTAATCTGTGTTTCCAGTTTCTAACAAAAATCTACAGGCTGGTGACTTTAGAGCTAAAGGTTGGAGCTGACCTGTAATCTCAAGGGCCAAGTGTTGAGAACCCTTGTTATAgatcagttatttttttaattcaagaaGTTTTCTGTTTTCAGTTGAAAACAATGTTGTGTAAACAGTCCCTTAATTCAGGTCTCCAGGATCAGAAACCAGTGGTATAGATTATTCCCATACATCTACAGTAATATCTGAtgttaatatcttttttttttttaacttatctaGTTGAACATGCCATTGCTGTTTTTACTGCCCTACCGCTGCTCTTCCCATCTGGGTCTGCAGCACCGAAGAAACAGGTCCCAATCAGTGAGGCTCTTTTCCATGTTCTGACGGTGAGTTTTACTTTAAGTAGTGATAAGTTAATAACAGGTGACTACATTGTCAATAAAATACTAAGTTAAAACCATCCCAATTGCACTACGTAAAATTGGACATGCAATGTAACAACTAACTTAAAGGTATTGtagaaatttttttaattatgtcttCATTTACTTAATCACaacctgctgaacacaaaagtaagatattttgaagaatgttgatatgCCAACCCAGATCTGTTGGGTTggcattcacttccattgaagaaaaaaaaatatggaagTGAATAGTGACCCAGATCTTATATTAATTTTTGCTGTGTTTGTAGTCTGAAttctgtatttttgttatttggttTTCTAGCCCTCAGAGGACCCGGATACCTACATCCACAGGCGTGCACTTTCCAGTCCTGTCTTGCTGGTTGGTGAGGAGAACTGCATGGTGGTTGTAGGTACAACCCCAGTTCTAACATTTGACAAAGACTTGCTCTATGAGGGGCCTCTCTACCTCCTGGCCTATTACTATGCATTTCATCTCACATATCCAAAGTGTCTTGCAACACTCCTGTCTGTGTTGCAAACACAAGTTCTGAGAGATGTCATCCACGAGCAGGATGAAACCCCCTCGTACAAAAAGGCCATTCATGAATGGAGAATGTTTGTTGACTAATTGCTGTTTCAAACTGCTGTGGCTGAGAGacagctgcatttttttttcggcCATTACATTTGCACTTGATTTGTGCTGTTAGGAGTTTTTCCCCATTTTCAGGAGATTAAATGTATCTAACATACAGTAATGCAGCACAGCAAAACCAAAAAAAGTAATTGCTGTGTGTAACTTTACAGGACTGCTGAGGGTATACAGTGTTGTTTTGTGCCAgagtatattttttgttgttattattaacgtTGGACTGTTCATCCTGTTTTGCTGTACCTCAGTTGTTTAAGagaaatgaaaatgttcatttttgaatcTGCCATGGATTCAAGGCATTGTTGACCCAAACTTCAATTACTTCCTAATCTtatgttgtttcaaacctgttttttttttcttttggctaCAGAAGATATTATTTAGAATGTTGGGAACTGTTGATGGtagctattgactttcatagtattttttttatttattttgtatatttttctagCTATGAAAGCTGGCGACATTCTTCAAAGTGTCgtcttctgcaaaaaaaaaaaaaaaaactcataaggATTTGAAGAACATAAGGGTGAGCAtgataattatttgatttttggGTTGCTATCATGTTACGAAATAAATTGATCCAGGCTGTTTGAAGCTTAAATGCTGTTTGAGTTTGTGTAGACTGAGGCAAAGCATTTTGCGTAGAATACTTGCGGTTTCTGTGCcaggtattttatttaattttaaagtgtaaGCTTGTCTTTGCTTATCCTGCCTTATGCTCCATTTGTTTAGAACTTTAAAGAATGTTCTTTAATAAATGTTCAGCAAAGCTGGAAGTTGTTTCTTCACTTAAAGTGGGGGAAGGTGTGGGAGGTACTTTCTTTTAAGAGTTTTCATCTCATTTAGGttttgtgtgatttaaaaaaaatctaaataggcTGGATTTAAGGTAAACTATTCTGCTTTCAATGCATTTTCCCCCTAAAATTATTATTGTCGTGCTTCAAAAAAGAGAAAACTGCTCAATTTTAAGCttgtttgtctagttttaagaactAACTGTAGATTTACTGACTAGATTTAAGTTCAAATATTCTAGTTTTAATGCAATTTGTTCTAGAATTATTCATGTTCAGtg

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:0001706 endoderm formation biological_process
GO:0048732 gland development 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: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:0007507 heart development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0010646 regulation of cell communication biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0043011 myeloid dendritic cell differentiation biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0001773 myeloid dendritic cell activation biological_process
GO:0003154 BMP signaling pathway involved in determination of left/right symmetry biological_process
GO:0035295 tube development biological_process
GO:0009059 macromolecule 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: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: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:0060974 cell migration involved in heart formation biological_process
GO:0060975 cardioblast migration to the midline involved in heart field formation biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:1903506 regulation of nucleic acid-templated transcription biological_process
GO:1901362 organic cyclic compound biosynthetic process biological_process
GO:0010468 regulation of gene expression biological_process
GO:0010470 regulation of gastrulation biological_process
GO:0023051 regulation of signaling biological_process
GO:0061008 hepaticobiliary system development biological_process
GO:0009966 regulation of signal transduction 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:0001889 liver development biological_process
GO:0003260 cardioblast migration biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0003002 regionalization 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: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:0072045 convergent extension involved in nephron morphogenesis biological_process
GO:0042663 regulation of endodermal cell fate specification biological_process
GO:0003318 cell migration to the midline involved in heart development 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:0097028 dendritic cell differentiation 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

Ensembl:

ensembl_id ENSDART00000194598

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00044660 lncRNA upstream 344 15478184 ~ 15478737 (+) True XLOC_021543
TCONS_00044797 lncRNA upstream 1244074 14233725 ~ 14235007 (+) True XLOC_021536
TCONS_00042774 lncRNA upstream 1336846 14097508 ~ 14142235 (+) False XLOC_021534
TCONS_00044796 lncRNA upstream 1537803 13928339 ~ 13941278 (+) False XLOC_021533
TCONS_00044795 lncRNA upstream 1628589 13844754 ~ 13850492 (+) True XLOC_021532
TCONS_00044662 lncRNA downstream 265873 15749752 ~ 15756516 (+) True XLOC_021545
TCONS_00044663 lncRNA downstream 530018 16013897 ~ 16017825 (+) True XLOC_021547
TCONS_00044798 lncRNA downstream 550359 16034238 ~ 16034588 (+) True XLOC_021548
TCONS_00044664 lncRNA downstream 584373 16068252 ~ 16071383 (+) True XLOC_021549
TCONS_00044799 lncRNA downstream 742552 16226431 ~ 16230571 (+) False XLOC_021550
TCONS_00042785 mRNA upstream 675280 14771979 ~ 14803801 (+) True XLOC_021541
TCONS_00042784 mRNA upstream 747189 14696043 ~ 14731892 (+) True XLOC_021540
TCONS_00042780 mRNA upstream 747600 14590483 ~ 14731481 (+) False XLOC_021540
TCONS_00042791 mRNA downstream 946680 16430559 ~ 16525698 (+) False XLOC_021555
TCONS_00042793 mRNA downstream 985651 16469530 ~ 16525698 (+) True XLOC_021555
TCONS_00042795 mRNA downstream 1136922 16620801 ~ 16642181 (+) False XLOC_021557
TCONS_00042794 mRNA downstream 1136922 16620801 ~ 16642181 (+) False XLOC_021557
TCONS_00042797 mRNA downstream 1150072 16633951 ~ 16642181 (+) False XLOC_021557
TCONS_00042786 other upstream 125832 15353133 ~ 15353249 (+) True XLOC_021542
TCONS_00042779 other upstream 1008510 14468003 ~ 14470571 (+) True XLOC_021539
TCONS_00042770 other upstream 1874761 13604218 ~ 13604320 (+) True XLOC_021527
TCONS_00042766 other upstream 2036359 13442608 ~ 13442722 (+) True XLOC_021525
TCONS_00042749 other upstream 3260706 12213967 ~ 12218375 (+) True XLOC_021513
TCONS_00042789 other downstream 266139 15750018 ~ 15751546 (+) True XLOC_021546
TCONS_00042790 other downstream 872829 16356708 ~ 16357229 (+) True XLOC_021553
TCONS_00042792 other downstream 961082 16444961 ~ 16446040 (+) True XLOC_021556
TCONS_00042812 other downstream 1375038 16858917 ~ 16859033 (+) True XLOC_021565
TCONS_00042818 other downstream 1414446 16898325 ~ 16901006 (+) False XLOC_021567

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000140_02075636_02092672.mRNA False 2345 mRNA 0.41 7 CI01000140 2074686 ~ 2093068 (+)
striped catfish (Pangasianodon hypophthalmus) TU225293 True 271 lncRNA 0.41 1 NC_047606.1 3497129 ~ 3497399 (-)
bowfin (Amia calva) AMCG00003834 True 309 mRNA 0.42 2 CM030121.1 19789393 ~ 19789825 (-)
tiger barb (Puntius tetrazona) TU225293 True 3075 TUCP 0.33 5 NC_056720.1 12045469 ~ 12049531 (-)