RNA id: TCONS_00055792


Basic Information

Item Value
RNA id TCONS_00055792
length 685
lncRNA type retained_intron
GC content 0.40
exon number 2
gene id XLOC_028790
representative True

Chromosome Information

Item Value
chromosome id NC_007115.7
NCBI id CM002888.2
chromosome length 78093715
location 25054510 ~ 25064510 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CTTAGGACCGCTAAGTTATTTGTTGATCTTATCAGGTGATGTCACATTTGACGATTGAGGAGTTAAGCTTAGTGATGTCATGCTAGATAATGTTTTTCATTTGGTAATGCATTAATAATagtcctaataataataataataataataataataatgttattaatgcatttcCAAATTCATACTTTTTTTATTAGTGCGACTCTTCAGCCTGTTTGTATTTTTGATATTGCATTTTCTTCACATTCCtatgaataattcattattattcttAATCTGTGTATTATTTGTGTATATTATTTGCATCATATTTAATCTGCAATAATTCTGTTCAATATAGCAAACGAGCGAATGGCCACTATGTTTATGCGCACCAGTGGCATGGGTTGTGTAGTTGTGCTTGCGTGTGCATGTAAGTTGTGTTTTAGTGGCTCTAAAAATGAGATGTGcatgcgtgtgtatctgtgttcgCAGAGGGTAGAGAATGTGTAAACTGCGGGGCCACCTCGACTCCTCTGTGGCGGAGGGATGGCACCGGTCACTATTTGTGTAACGCCTGCGGACTTTACCACAAGATGAACGGACAGAACCGACCCCTCATCAAGCCCAAACGGAGGCTGTCTGCTGCCAGACGAGCTGGGACCTCATGCGCAAACTGTCAAACGACCACGACGACACTGTGGCGGAG

Function

GO:

id name namespace
GO:0002520 immune system development biological_process
GO:2001224 positive regulation of neuron migration biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0043049 otic placode formation biological_process
GO:0045165 cell fate commitment biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0048568 embryonic organ development biological_process
GO:0045582 positive regulation of T cell differentiation biological_process
GO:0008543 fibroblast growth factor receptor signaling pathway biological_process
GO:0042246 tissue regeneration biological_process
GO:0031101 fin regeneration biological_process
GO:0008284 positive regulation of cell population proliferation biological_process
GO:0071696 ectodermal placode development biological_process
GO:0061026 cardiac muscle tissue regeneration biological_process
GO:0050769 positive regulation of neurogenesis biological_process
GO:0030856 regulation of epithelial cell differentiation biological_process
GO:0060788 ectodermal placode formation biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0048702 embryonic neurocranium morphogenesis biological_process
GO:0021514 ventral spinal cord interneuron differentiation biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003677 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: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:0008270 zinc ion binding molecular_function

KEGG:

id description
ko04658 Th1 and Th2 cell differentiation
ko04659 Th17 cell differentiation
ko04928 Parathyroid hormone synthesis, secretion and action
ko05321 Inflammatory bowel disease
ko03000 Transcription factors

ZFIN:

id description
ZDB-GENE-990415-82 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including fibroblast growth factor receptor signaling pathway; positive regulation of neurogenesis; and positive regulation of neuron migration. Acts upstream of or within several processes, including cardiac muscle tissue regeneration; embryonic organ morphogenesis; and fin regeneration. Predicted to be located in nucleus. Is expressed in several structures, including digestive system; ectoderm; nervous system; neural tube; and pleuroperitoneal region. Used to study hypoparathyroidism-retardation-dysmorphism syndrome. Human ortholog(s) of this gene implicated in hypoparathyroidism; hypoparathyroidism-deafness-renal disease syndrome; nephrosis; and sensorineural hearing loss. Orthologous to human GATA3 (GATA binding protein 3).

Ensembl:

ensembl_id ENSDART00000149971

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00057356 lncRNA downstream 9468 24971644 ~ 25049007 (-) True XLOC_028789
TCONS_00058216 lncRNA downstream 9605 24924363 ~ 25048870 (-) False XLOC_028789
TCONS_00057355 lncRNA downstream 86394 24833526 ~ 24972081 (-) False XLOC_028789
TCONS_00057354 lncRNA downstream 211498 24833526 ~ 24846977 (-) False XLOC_028789
TCONS_00058215 lncRNA downstream 267734 24726095 ~ 24790741 (-) True XLOC_028788
TCONS_00058217 lncRNA upstream 184295 25245031 ~ 25247848 (-) True XLOC_028794
TCONS_00055803 lncRNA upstream 413470 25474206 ~ 25478126 (-) False XLOC_028796
TCONS_00055804 lncRNA upstream 413470 25474206 ~ 25479379 (-) True XLOC_028796
TCONS_00058218 lncRNA upstream 433720 25494456 ~ 25497067 (-) True XLOC_028797
TCONS_00055817 lncRNA upstream 945706 26006442 ~ 26007456 (-) True XLOC_028804
TCONS_00055787 mRNA downstream 1026551 23886726 ~ 24031924 (-) False XLOC_028785
TCONS_00055790 mRNA downstream 1026719 23888549 ~ 24031756 (-) True XLOC_028785
TCONS_00055786 mRNA downstream 1038764 23886726 ~ 24019711 (-) False XLOC_028785
TCONS_00055785 mRNA downstream 1094635 23886726 ~ 23963840 (-) False XLOC_028785
TCONS_00055784 mRNA downstream 1094637 23886726 ~ 23963838 (-) False XLOC_028785
TCONS_00055793 mRNA upstream 23492 25084228 ~ 25168458 (-) True XLOC_028791
TCONS_00055794 mRNA upstream 112563 25173299 ~ 25181552 (-) True XLOC_028792
TCONS_00055796 mRNA upstream 127176 25187912 ~ 25215968 (-) False XLOC_028793
TCONS_00055795 mRNA upstream 127176 25187912 ~ 25215968 (-) True XLOC_028793
TCONS_00055797 mRNA upstream 191119 25251855 ~ 25271455 (-) False XLOC_028795
TCONS_00055780 other downstream 1304204 23746043 ~ 23754271 (-) True XLOC_028783
TCONS_00055776 other downstream 1606544 23451817 ~ 23451931 (-) True XLOC_028782
TCONS_00055774 other downstream 1639020 23419320 ~ 23419455 (-) True XLOC_028780
TCONS_00055773 other downstream 1831626 23226733 ~ 23226849 (-) True XLOC_028779
TCONS_00055755 other downstream 2821181 22236358 ~ 22237294 (-) True XLOC_028767
TCONS_00055802 other upstream 413470 25474206 ~ 25478995 (-) False XLOC_028796
TCONS_00055813 other upstream 780050 25840786 ~ 25840902 (-) True XLOC_028802
TCONS_00055827 other upstream 1346410 26407146 ~ 26407263 (-) True XLOC_028811
TCONS_00055829 other upstream 2027635 27088371 ~ 27099285 (-) True XLOC_028815
TCONS_00055832 other upstream 2080443 27141179 ~ 27141303 (-) True XLOC_028817

Expression Profile

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