RNA id: TCONS_00028947


Basic Information

Item Value
RNA id TCONS_00028947
length 851
lncRNA type retained_intron
GC content 0.50
exon number 3
gene id XLOC_014648
representative True

Chromosome Information

Item Value
chromosome id NC_007130.7
NCBI id CM002903.2
chromosome length 48449771
location 14187540 ~ 14191592 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

AACAGTCGGTGGCTGGTTCCTGCCCAGTAACGGCCCCATGGGCCCCAGCAGCAGCCCTCCTCAGTTCAATGGGGCCCCTGTTCACTCCTCGGGTTCGTACTGTGAGAGATACTCCAGCTTGAGGAACCACAGAGCTGCTCCATATCCCAGCCATTACTCCCACCGCAGCACTACCACCAATAACTACATGGACAACTCTTCCGGAAGTCTTGCGTCTCATGACAGCTGGTCAGCCCTGCAGATCCCCAACTCCAGCGGGATGGGAACCCTGGCCCACACCACAAACACTACCTCCAACACCAGTCAGTACCCAAGTCTGTGGTCAGTTGCAGGGACGACTCTCACCCCATCAGGCTCAGCATCGGGCTCCATTACAGGTGGCCTGACATCTCAGTTCCTACGCGGTTCTTCGATGTCCTACTCGGGTCTGACCTCCTCGCTGCCTGTGTCCTCTCCCTCCTCAATGTACGATCCAGGCCTAAGCGAGGTTGGCGTTGGAGATGCCCAGTTCGAGAGCTCCATCGCCCGGCTCACAGCATCATGGGCGCCTGTGGCTCAGAGCTACTGAGATCGCTTCACATTTAAGGACTGATGCTGCAGTTATGGACTTGATCTTGGCTTCAGGAGGAAATCTAGAAGAGCTTCTTGATTTGACAATCAGAAAACGGGTTGATTTACTATAAAAGTCACATCTGTATCATACCGAGGCATACGTATTTACAATCAAGATGAGAGACAAtcaattaaagggttagttcttgcaaaaaagaaaattttgacatcatttactcacctttgttttaaacattgttaagtttttattctgttaaacacaaaagaagatattttga

Function

GO:

id name namespace
GO:0001707 mesoderm formation biological_process
GO:0001708 cell fate specification biological_process
GO:0035775 pronephric glomerulus morphogenesis biological_process
GO:0007498 mesoderm development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0001756 somitogenesis biological_process
GO:0036342 post-anal tail morphogenesis biological_process
GO:0003140 determination of left/right asymmetry in lateral mesoderm biological_process
GO:0003143 embryonic heart tube morphogenesis biological_process
GO:0031016 pancreas development biological_process
GO:2000223 regulation of BMP signaling pathway involved in heart jogging biological_process
GO:0007275 multicellular organism development biological_process
GO:0010159 specification of animal organ position biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0048565 digestive tract development biological_process
GO:0070121 Kupffer's vesicle development biological_process
GO:0014028 notochord formation biological_process
GO:0007368 determination of left/right symmetry biological_process
GO:0001889 liver development biological_process
GO:0003007 heart morphogenesis biological_process
GO:0061053 somite development biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0060028 convergent extension involved in axis elongation biological_process
GO:0060034 notochord cell differentiation biological_process
GO:0030903 notochord development biological_process
GO:0001947 heart looping biological_process
GO:0035462 determination of left/right asymmetry in diencephalon biological_process
GO:0072045 convergent extension involved in nephron morphogenesis biological_process
GO:0042663 regulation of endodermal cell fate specification biological_process
GO:0016055 Wnt signaling pathway biological_process
GO:0061371 determination of heart left/right asymmetry biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0005515 protein 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: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

KEGG: NA

ZFIN:

id description
ZDB-GENE-980526-437 Enables transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including Kupffer's vesicle development; animal organ development; and post-anal tail morphogenesis. Located in chromatin and nucleus. Is expressed in several structures, including blastoderm; germ ring; mesoderm; presumptive structure; and tail bud. Human ortholog(s) of this gene implicated in neural tube defect. Orthologous to human TBXT (T-box transcription factor T).

Ensembl:

ensembl_id ENSDART00000170286

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00030177 lncRNA downstream 121570 14062042 ~ 14066550 (-) True XLOC_014646
TCONS_00028942 lncRNA downstream 254934 13928251 ~ 13933186 (-) True XLOC_014643
TCONS_00028940 lncRNA downstream 265016 13919007 ~ 13923104 (-) True XLOC_014642
TCONS_00030176 lncRNA downstream 731125 13452858 ~ 13456995 (-) False XLOC_014639
TCONS_00030179 lncRNA upstream 1836807 16026893 ~ 16030742 (-) False XLOC_014657
TCONS_00030178 lncRNA upstream 1836807 16026893 ~ 16030742 (-) False XLOC_014657
TCONS_00030180 lncRNA upstream 1836807 16026893 ~ 16030745 (-) False XLOC_014657
TCONS_00030182 lncRNA upstream 1836807 16026893 ~ 16030750 (-) False XLOC_014657
TCONS_00030181 lncRNA upstream 1836807 16026893 ~ 16030750 (-) False XLOC_014657
TCONS_00028945 mRNA downstream 32339 14153486 ~ 14155781 (-) True XLOC_014647
TCONS_00028944 mRNA downstream 225651 13961396 ~ 13962469 (-) True XLOC_014645
TCONS_00028943 mRNA downstream 237889 13939750 ~ 13950231 (-) True XLOC_014644
TCONS_00028941 mRNA downstream 254916 13923600 ~ 13933204 (-) False XLOC_014643
TCONS_00028938 mRNA downstream 265029 13905068 ~ 13923091 (-) False XLOC_014642
TCONS_00028948 mRNA upstream 713293 14903379 ~ 14970813 (-) True XLOC_014649
TCONS_00028949 mRNA upstream 713530 14903616 ~ 14968192 (-) True XLOC_014650
TCONS_00028950 mRNA upstream 952441 15142527 ~ 15229421 (-) False XLOC_014651
TCONS_00028951 mRNA upstream 954422 15144508 ~ 15177324 (-) False XLOC_014651
TCONS_00028952 mRNA upstream 984389 15174475 ~ 15192840 (-) False XLOC_014651
TCONS_00028935 other downstream 413651 13733168 ~ 13774469 (-) True XLOC_014640
TCONS_00028926 other downstream 1554857 12633149 ~ 12633263 (-) True XLOC_014634
TCONS_00028921 other downstream 1795362 12386297 ~ 12392758 (-) True XLOC_014630
TCONS_00028910 other downstream 2042355 12134847 ~ 12145765 (-) True XLOC_014624
TCONS_00028954 other upstream 984757 15174843 ~ 15192646 (-) True XLOC_014651
TCONS_00028962 other upstream 1837333 16027419 ~ 16027490 (-) True XLOC_014658
TCONS_00028963 other upstream 1838370 16028456 ~ 16028590 (-) True XLOC_014659
TCONS_00028964 other upstream 1839222 16029308 ~ 16029443 (-) True XLOC_014660
TCONS_00028972 other upstream 2809541 16999627 ~ 16999742 (-) True XLOC_014664

Expression Profile

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