RNA id: TCONS_00042978


Basic Information

Item Value
RNA id TCONS_00042978
length 764
lncRNA type inter_gene
GC content 0.38
exon number 2
gene id XLOC_021651
representative True

Chromosome Information

Item Value
chromosome id NC_007134.7
NCBI id CM002907.2
chromosome length 46223584
location 21473102 ~ 21474482 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATTGAATTTCACTGAGCACTGAAGAACGACAATCCTTCGCCATGAGAGATCTGCAGAAAACGTGTAAAATTGTGAGCCTGGAAAGGAAATGCTCAGATGGTGTAGAGCAGTTTCTGGGTGTTTTGGAGCAGCGGCTGCACAATGGCATCTCTCCCACTGAGCTTTGGGACAAAACCCTCTCGTTCTTCACCCCAAAGAAGACCTTGATCTTCCACAATGGATACTCCAAGTACTCCAGGGAGACGCTTCGGTTGTTTCCAGACTCTGCAGAAGACGTGTCTCCTCTTTGCATTCAGCAGTGACACAAACATATGTTGTGGAAGAGATGGAAGTTCTTTGGTCAAGTCTTGGTCTTCAGAATTGCTGAACTGAACTTGGTTTTTCTGCTGGACATGGAGGCATGATTTttctgtctctttttttaaaatacagcagCATATTAATGAAGAAAAGTCTTTTATAAAGACATGATGTGCataaaaacaaatggtaccctaaGGGGGTTTTGTATTCCAGAAATGGATTTATGATAGGATTTGTTGTAATGCCAACAATTGTGCGTAATTGCTTTTGATGCAATATACAGAGAAAAATGATATCATGAGTTTGCTAAATGATAAACCTGACACTAAAGTTATTTAAGAATAGAATATGTTTGTCTGCTGTTTTATGCAATGGATTGTGTTAGTCTGAATGCTTAAATGCATTTGCTAATGATTTAATCAGATGtttgttaacaaaataaaattcttTCCTAAAATTTG

Function

GO:

id name namespace
GO:0048731 system development biological_process
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0016070 RNA metabolic process biological_process
GO:0048468 cell 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:0007219 Notch signaling pathway 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:0030154 cell differentiation biological_process
GO:0006942 regulation of striated muscle contraction biological_process
GO:0048513 animal organ development biological_process
GO:1990399 epithelium regeneration biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0009058 biosynthetic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:0030182 neuron differentiation biological_process
GO:1901576 organic substance biosynthetic process biological_process
GO:0007275 multicellular organism development biological_process
GO:0009888 tissue development biological_process
GO:0009889 regulation of biosynthetic process biological_process
GO:0002065 columnar/cuboidal epithelial cell differentiation biological_process
GO:0009891 positive 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:0031326 regulation of cellular biosynthetic process biological_process
GO:0031328 positive regulation of cellular biosynthetic process biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:1902680 positive regulation of RNA biosynthetic process biological_process
GO:0051239 regulation of multicellular organismal process biological_process
GO:0009653 anatomical structure morphogenesis biological_process
GO:0048856 anatomical structure development biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:0006725 cellular aromatic compound metabolic process biological_process
GO:0051254 positive regulation of RNA metabolic process biological_process
GO:0006729 tetrahydrobiopterin biosynthetic 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:1903508 positive regulation of nucleic acid-templated transcription biological_process
GO:0010467 gene expression biological_process
GO:0010468 regulation of gene expression biological_process
GO:0042559 pteridine-containing compound biosynthetic process biological_process
GO:0048869 cellular developmental process biological_process
GO:0045595 regulation of cell differentiation biological_process
GO:2000026 regulation of multicellular organismal development biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0043696 dedifferentiation biological_process
GO:0034312 diol biosynthetic process biological_process
GO:0043697 cell dedifferentiation biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0046146 tetrahydrobiopterin metabolic process biological_process
GO:0045893 positive regulation of transcription, DNA-templated biological_process
GO:0050767 regulation of neurogenesis biological_process
GO:0070654 sensory epithelium regeneration biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0003002 regionalization biological_process
GO:0007389 pattern specification process biological_process
GO:0050793 regulation of developmental process biological_process
GO:0007399 nervous system development biological_process
GO:0048934 peripheral nervous system neuron differentiation biological_process
GO:0048935 peripheral nervous system neuron development biological_process
GO:0032501 multicellular organismal process biological_process
GO:0048936 peripheral nervous system neuron axonogenesis biological_process
GO:2001141 regulation of RNA biosynthetic process biological_process
GO:0032502 developmental process biological_process
GO:0045935 positive regulation of nucleobase-containing compound metabolic process biological_process
GO:0032774 RNA biosynthetic process biological_process
GO:0060284 regulation of cell development biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0019438 aromatic compound biosynthetic process biological_process
GO:0007417 central nervous system development biological_process
GO:0010556 regulation of macromolecule biosynthetic process biological_process
GO:0010557 positive regulation of macromolecule biosynthetic process biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0060290 transdifferentiation biological_process
GO:0007420 brain development biological_process
GO:0007422 peripheral nervous system development biological_process
GO:0034654 nucleobase-containing compound biosynthetic process biological_process
GO:0022008 neurogenesis biological_process
GO:2000112 regulation of cellular macromolecule biosynthetic process biological_process
GO:0048699 generation of neurons biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0042668 auditory receptor cell fate determination biological_process
GO:0021510 spinal cord development biological_process
GO:0060322 head development biological_process
GO:0021515 cell differentiation in spinal cord biological_process
GO:0021517 ventral spinal cord development biological_process
GO:0051960 regulation of nervous system development biological_process
GO:0005901 caveola cellular_component
GO:0005634 nucleus cellular_component
GO:0044853 plasma membrane raft cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0005488 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:0000978 RNA polymerase II cis-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:0000987 cis-regulatory region sequence-specific DNA binding molecular_function
GO:0140110 transcription regulator activity molecular_function
GO:0046983 protein dimerization 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_00042967 lncRNA upstream 99174 21371236 ~ 21373932 (+) True XLOC_021647
TCONS_00042966 lncRNA upstream 105885 21364074 ~ 21367221 (+) False XLOC_021647
TCONS_00042963 lncRNA upstream 195584 21261390 ~ 21277522 (+) True XLOC_021646
TCONS_00042949 lncRNA upstream 779958 20687391 ~ 20693148 (+) False XLOC_021638
TCONS_00042989 lncRNA downstream 307095 21781577 ~ 21783450 (+) True XLOC_021659
TCONS_00044671 lncRNA downstream 431571 21906053 ~ 21914926 (+) False XLOC_021660
TCONS_00044815 lncRNA downstream 431577 21906059 ~ 21909458 (+) True XLOC_021660
TCONS_00042995 lncRNA downstream 580094 22054576 ~ 22058438 (+) True XLOC_021662
TCONS_00043001 lncRNA downstream 860943 22335425 ~ 22344252 (+) True XLOC_021664
TCONS_00042977 mRNA upstream 11966 21459263 ~ 21461140 (+) True XLOC_021650
TCONS_00042975 mRNA upstream 11972 21455152 ~ 21461134 (+) False XLOC_021650
TCONS_00042974 mRNA upstream 11972 21455152 ~ 21461134 (+) False XLOC_021650
TCONS_00042973 mRNA upstream 12029 21455152 ~ 21461077 (+) False XLOC_021650
TCONS_00042979 mRNA downstream 5476 21479958 ~ 21490515 (+) False XLOC_021652
TCONS_00042980 mRNA downstream 5608 21480090 ~ 21488083 (+) False XLOC_021652
TCONS_00042981 mRNA downstream 8089 21482571 ~ 21490515 (+) True XLOC_021652
TCONS_00042982 mRNA downstream 17669 21492151 ~ 21498974 (+) True XLOC_021653
TCONS_00042983 mRNA downstream 69745 21544227 ~ 21563055 (+) True XLOC_021654
TCONS_00042958 other upstream 358374 21067389 ~ 21114732 (+) False XLOC_021644
TCONS_00042937 other upstream 1001236 20471755 ~ 20471870 (+) True XLOC_021632
TCONS_00042936 other upstream 1002511 20448905 ~ 20470595 (+) True XLOC_021631
TCONS_00042927 other upstream 1285367 20187625 ~ 20187739 (+) True XLOC_021627
TCONS_00042922 other upstream 1651643 19813719 ~ 19821463 (+) False XLOC_021624
TCONS_00042986 other downstream 149253 21623735 ~ 21623849 (+) True XLOC_021656
TCONS_00043003 other downstream 1116576 22591058 ~ 22591155 (+) True XLOC_021666
TCONS_00043017 other downstream 1546227 23020709 ~ 23049140 (+) False XLOC_021673
TCONS_00043030 other downstream 2597547 24072029 ~ 24072110 (+) True XLOC_021680
TCONS_00043031 other downstream 2597678 24072160 ~ 24072245 (+) True XLOC_021681

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) TU20029 True 642 lncRNA 0.48 2 CI01000001 6948630 ~ 6949373 (-)