RNA id: TCONS_00019752


Basic Information

Item Value
RNA id TCONS_00019752
length 897
lncRNA type retained_intron
GC content 0.42
exon number 4
gene id XLOC_009898
representative False

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 23960744 ~ 23963461 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CACGCTTCTCAGGTGTTCTTGTCTGTCCATCAACATGAGGTCTCTTGTGGTATTCTTTGCTCTGGCAGTTTTAACtgGCTGCCAGGCTCGTAGCCTGTTCCAGGCTGATGCCCCTCAGCCCAGATGGGAGGAGATGGTGGACCGTTTCTGGCAGTATGTGTCTGAACTCAACACACAAACTGACGGCATGGTGCAAAACATCAAGGGCTCCCAGCTCAGCAGAGAGCTTGACACACTAATTACTGACACCATGGCTGAACTGAGCTCATACAGTGAAAATCTCCAAACCCAGATGACCCCATACGCCTCTGATGCTGCTGGTCAGCTCAGTAAAGATCTTCAGCTCCTGGCTGGAAAACTCCAAACTGACATGACCGACGCTAAGGAACGCAGCACTCAGTACCTGCAAGAGCTGAAGACCATGATGGAGCAGAATGCAGATGACGTGAAGAACCGTGTCGGCACCTACACACGCAAACTGAAGAAACGCCTGAACAAGGACACAGAGGAGATCCGCAAGTAAGTTGGGATGCTCCTTCAGGTGGCTTACGagaaaaccctttttttttttttttttttttagctatttttgGTATTATTTAATCCATTCACGTCCAGGTCTGGCCAGAgaaacttttagcttagcataaattatagAATCAAatttgaccattagcatcttgctcaaaaaaaaaaaaaagagttttgataaattTCCTTTTAAAGCTTGcttcttctgtagttacatcatgtattaagacctacataaaaataaacgttgctattttctaggcaaatatatctagtaaaagataAGCGTAAAGCTTAAAATAGAAAACTCTTTGAGCGCAATGCTAATAGTTTAACCCgcttcaataatctatgctaaaatAAGAT

Function

GO:

id name namespace
GO:0034447 very-low-density lipoprotein particle clearance biological_process
GO:0071831 intermediate-density lipoprotein particle clearance biological_process
GO:1900221 regulation of amyloid-beta clearance biological_process
GO:0042157 lipoprotein metabolic process biological_process
GO:0042158 lipoprotein biosynthetic process biological_process
GO:0042159 lipoprotein catabolic process biological_process
GO:0006707 cholesterol catabolic process biological_process
GO:0051000 positive regulation of nitric-oxide synthase activity biological_process
GO:0034380 high-density lipoprotein particle assembly biological_process
GO:0034382 chylomicron remnant clearance biological_process
GO:0033344 cholesterol efflux biological_process
GO:0043524 negative regulation of neuron apoptotic process biological_process
GO:0006869 lipid transport biological_process
GO:0031012 extracellular matrix cellular_component
GO:0005576 extracellular region cellular_component
GO:0005615 extracellular space cellular_component
GO:0034361 very-low-density lipoprotein particle cellular_component
GO:0034362 low-density lipoprotein particle cellular_component
GO:0034363 intermediate-density lipoprotein particle cellular_component
GO:0034364 high-density lipoprotein particle cellular_component
GO:0008201 heparin binding molecular_function
GO:0042802 identical protein binding molecular_function
GO:0043395 heparan sulfate proteoglycan binding molecular_function
GO:0050750 low-density lipoprotein particle receptor binding molecular_function
GO:0008289 lipid binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-980526-368 Predicted to enable several functions, including heparan sulfate proteoglycan binding activity; heparin binding activity; and low-density lipoprotein particle receptor binding activity. Predicted to be involved in several processes, including cholesterol catabolic process; lipoprotein metabolic process; and triglyceride-rich lipoprotein particle clearance. Predicted to act upstream of or within lipid transport and lipoprotein metabolic process. Predicted to be located in extracellular matrix and extracellular space. Predicted to be part of high-density lipoprotein particle; low-density lipoprotein particle; and triglyceride-rich plasma lipoprotein particle. Is expressed in several structures, including digestive system; epidermis; fin bud; median fin; and nervous system. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease (multiple); artery disease (multiple); biliary tract cancer (multiple); eye disease (multiple); and familial hyperlipidemia (multiple). Orthologous to human APOE (apolipoprotein E).

Ensembl:

ensembl_id ENSDART00000133484

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00019749 lncRNA upstream 12816 23947289 ~ 23948093 (+) True XLOC_009897
TCONS_00019740 lncRNA upstream 45782 23914082 ~ 23915127 (+) True XLOC_009894
TCONS_00021929 lncRNA upstream 139163 23811601 ~ 23821746 (+) False XLOC_009891
TCONS_00019712 lncRNA upstream 663703 23294686 ~ 23297206 (+) True XLOC_009879
TCONS_00019708 lncRNA upstream 1084814 22872860 ~ 22876095 (+) True XLOC_009877
TCONS_00019763 lncRNA downstream 16909 23979380 ~ 23980174 (+) True XLOC_009900
TCONS_00021711 lncRNA downstream 22284 23984755 ~ 23991159 (+) False XLOC_009901
TCONS_00019766 lncRNA downstream 22306 23984777 ~ 23991098 (+) False XLOC_009901
TCONS_00021930 lncRNA downstream 22783 23985254 ~ 23991098 (+) True XLOC_009901
TCONS_00021931 lncRNA downstream 56637 24019108 ~ 24028618 (+) False XLOC_009902
TCONS_00019748 mRNA upstream 12371 23947213 ~ 23948538 (+) False XLOC_009897
TCONS_00019745 mRNA upstream 12478 23947196 ~ 23948431 (+) False XLOC_009897
TCONS_00019746 mRNA upstream 12631 23947197 ~ 23948278 (+) False XLOC_009897
TCONS_00019747 mRNA upstream 12867 23947203 ~ 23948042 (+) False XLOC_009897
TCONS_00019743 mRNA upstream 36064 23923746 ~ 23924845 (+) False XLOC_009896
TCONS_00019755 mRNA downstream 9655 23972126 ~ 23973718 (+) False XLOC_009899
TCONS_00019756 mRNA downstream 9655 23972126 ~ 23973721 (+) True XLOC_009899
TCONS_00019757 mRNA downstream 13459 23975930 ~ 23977128 (+) False XLOC_009892
TCONS_00019758 mRNA downstream 13527 23975998 ~ 23977128 (+) False XLOC_009892
TCONS_00019759 mRNA downstream 13601 23976072 ~ 23977118 (+) False XLOC_009892
TCONS_00019735 other upstream 106298 23837920 ~ 23854611 (+) False XLOC_009892
TCONS_00019728 other upstream 353557 23607231 ~ 23607352 (+) True XLOC_009889
TCONS_00019718 other upstream 561749 23397801 ~ 23399160 (+) False XLOC_009882
TCONS_00019682 other upstream 2257230 21699006 ~ 21703679 (+) False XLOC_009863
TCONS_00019667 other upstream 3047425 20913413 ~ 20913484 (+) True XLOC_009854
TCONS_00019767 other downstream 553621 24516092 ~ 24517092 (+) False XLOC_009904
TCONS_00019777 other downstream 918651 24881122 ~ 24881218 (+) True XLOC_009911
TCONS_00019779 other downstream 935700 24898171 ~ 24898253 (+) True XLOC_009912
TCONS_00019780 other downstream 943085 24905556 ~ 24918957 (+) True XLOC_009913
TCONS_00019788 other downstream 1133012 25095483 ~ 25096562 (+) False XLOC_009919

Expression Profile

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