RNA id: TCONS_00049849


Basic Information

Item Value
RNA id TCONS_00049849
length 4776
RNA type mRNA
GC content 0.41
exon number 18
gene id XLOC_025240
representative True

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 19299309 ~ 19323689 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATGGAGATCTCATTCATGCTTTTATTGGCGGTTACGTTATTCTGTCCCGTTCAGTCAGGTGCCTTGACTTGTGATTCACGGCAGTATCAGTGTGGCAATGGAAAGTGCATCACGGCGAGATGGGTGTGTGATGAAACTGATGACTGTGGTGATGGCACTGATGAACTTCCTGCTGCATGCTTGGCCAAGACCTGCAGACCCAGTCAGTTCAGTTGTGGTGGTCGACTAAACCAGTGTATTCCCAAGAGCTGGAAATGTGACGGAAAAGCAGATTGTGAGAATAATGCGGATGAGGAAGGCTGCGATCCTCGGCAGTGTCACGATGGAGAATTCCGTTGTGGCAGTGGTCAGTGCGTTACGGCTGCATTCGTGTGCGATGATGAGATAGACTGTGAAGATGGCAGTGATGAAGTCTCCTGTCCTCCAACCACGTGTGGCTCCAGCTCCTTCAGGTGCAACAACGCCCAGTGTGTCCCACGACTCTGGGTGTGCGATGGAGATGCCGACTGTGCCGACAATTCAGATGAGTTGCCTGAAAAATGTGGCCCTGGAACATCTAAGCCCACCAAAAATCCCTGCACTTCCATGGAGTTCCATTGCGGAAGTGGGGAATGCATACACGGTAGCTGGAAGTGTGATGGAGGAGCGGATTGTTTGGATCACTCGGATGAGCAAAACTGCTCCTTGCCAACATGCCGTCCAGATGAGTTCCAGTGTGGTGATGGGTCTTGCATCCACGGCAGTCGGCAGTGCAACCACGTTTATGACTGCAAAGACATGAGCGATGAGCTGGGCTGCGTCAATGCAACTCACTGTGAGCCACCATACAGGTTTAAGTGCCGCAGCGGTGAATGCATAAGCATGGAAAAGGTTTGCAACAAGCAACGGGACTGCAGGGATTGGTCTGATGAGCCGCTACGAGAATGTGACTCTAATGAGTGTCTTTACAACAACGGTGGCTGCTCTCATATCTGTAATGACCTGAAGATTGGTTATGAGTGCTTATGTCCTACTGGCTTCCGGTTGGTGGACAAGAGACGCTGTGAAGACATCGATGAGTGTGCCAACCCAGACACCTGCAGCCAAATCTGTGTCAACCAGATGGGTAGTTATAAGTGTGAGTGTGAGGATGGCTACCAGATGGACCCAGCCAGCAAGGCCTGCAAAGCTATTGGAACTATCGCCTACCTATTTTTCACCAATCGCCATGAAGTAAGGAAGATGACTCTGGATCGCAGTGAATACATACGCGTCATCCCCCGCCTGAAGAACGTTGTTGCACTAGACATGAATATTGCTTCCAGAGATATCTACTGGTCGGATTTATccctgaaaaaaatatacagAGCCCCAATGGATACAGCGGACAACTCATCCCAACACAGCATTGTGGTTGGCAGTGACTTAGATGCACCAGAAGGTATCGCAGTGGACTGGATCCATGGAAACATCTACTGGACGGACAGCATCAGGGGCGCCATCTCTGTGGCAACAGCTGACGGAAGCAGACGCAAGACGCTCTTCAAAGAGAACCTGGCCAAACCACGTGCCATTGTTGTCGACCCAATTAAAAACTTCATGTTCTGGACCGATTGGGGCACACCAGCCAAGATCGAAAAAAGTGGTCTTAATGGAGTTGACCGGAGCACTCTAGTTGCGGACGACATTGTGTGGCCCAATGGAATAACCCTAGACCTATTGACCGAGCGTCTGTACTGGGTTGACTCCAAACTCCATACTCTTTCCAGCATCAGTGTGCAGGGAGATGGTCGGCGTACTCTAATCATTGACCAAGGCAAACTTGCGCACCCTCTGAGTCTCACTGTTTTTGAGGAGAAAGTGTTTTGGACGGATGTAAGCAATAACGCCATTTTAAGTGCGAACCGCGTCACCGGAGGAGACATCACAAAAGTGGCCGAACACCTCTCATCTCCAGAGGACATTGTTCTTTTCCACAACCTCAAACAACCTACTGGAATCAACTGGTGCAGGATCAATAACGGTGGCTGTGAGTTCTTGTGCCTTGCTGCCCCTCAGATTAACAGATTCTCACCCAAATACACATGTGCCTGTCCAGATAATATGATGTTGGCCAGAGATATGCGGAAATGTGTACCAGcTGTAGTGACAGCTGCAACTCCTGTCAGGCCTGAAATACCCACAACCATTCGTCCTCAAGTTCCTTCAGAAACGACACCAAAACCTGCTAGGCCTTCCACTACCAATTCACAACCTTTACCTACTCCGGCTCCCAAGATCCCTAACAGACCCACTCAAGCTGCCACTTTGGTGCCTTCACAGGCCACAACTAAACTTCCCTTTTTCACCCAGACAGATGTCCACTTTGGTGATGTTAAGGCTGTCTCTGATACGTCATCTTCCACACTGTGGGCCTTGTATATTGTGGTTCCTCTTGCACTCCTCTGTTTGGTTGTGGGTGGcgctgcactgttttggagaaaatGGCGTCAGAAAAATACCAACAGCATCCACTTTGACAACCCGGTTTATCAGAAGACCACAGAGGACCAGGTGCATTTATGCAGAAACAACAGTTCTGATGGCTATTTTTACCCTCAGAGACAGACTGTGAGTCTGGATGATGAAATCTGATGATGAACTTGTTGAAACGATCCATGCTGAAACTGACAATGTTTCAAGACTGGAGGCAGTTTATACAGTTTTTACCTACACGGAGGTCAGTTCTTCAGCAAAACAGCATTTGGGGAACAATAGAGAACCAAACCGCCTTTCCACCCACACAAGACattcaatgcaaaaaaacaacaatccaGTGCTGACAATTCAGGGAAAACCAAACTGAAAACAAAGAAACCTCAGACAACAACAAGAACCTCGGCTTATCAAGGCAACTTAGCACTTCACTATATAGAAATTATATAGCAATCCACTTAACAGCACTTAAAAATGGAGGGCTTATCCTTATCAGATGTCCATAGGTTATTGTAGATAGTGTATGTATTAGTACATTTTAAAGAGttgcttttatttgtattttaaaagttttcAGAGGCATCAAAAACCTTTATCCAAAACATTTGTATTGTTTGGTTCATGCAGTATAGTAATTGAAGATGCAGTATGTGTTAATATATTTAGGATAGTACATTTACTGACATAGGATGTGCAAAGTTTATTTTCCTAAACATGTCTTGTTTTTATTCTTAGGTCAGCAATGCATTTAAAACTTATGGAAGCCAGTTCCACtgagtaaaaattaaataaataagtaaataaatacaatacaaaaaaaagttataaaatcagaattctgagttataaagttaaaattctgagttataaaatgGGAAGTCTAAGTTATAAAGTTGCAATTTTGAGTTACATAATAAGTtaactcgtaattctgacttaataactcgcaattctgaatTAATAACTTACAATTCTGACTAAATAATtgggaattctgacttaataactcgcaattctgacttaataactcgcaattctgacttaataattggaaattctgacttaacttgcaattctgacttaataactcgcaattctgacttaataactcgcaattctgacttaataactcgcaattctgacttaataattgggaattctgacttaataactcgcagttctgacttaataactcccAATTCTAACTAAATAACTACCATAAACTCACAATTCTAacttaactcgcaattctgacctaataactcggaattctgattTAACtctcaattctgacttaataatttgcaattctgactttataactcgtaattctgacttaataactcgcaattctgacttaatatcatggaattttgacTTCATAACTTGcatttctgactttataactggaaattctgacttaataacttggaattttgattttataactcaaaattctgacttaataactcgcaattctgacttaataacttcgAATTTTAACTTTATAACTTGCATTTCTCACTTTATAACTCCCaaatctgactttataactcgcaattttGACTTAATAACTCTGAATTCTTACTTTTTATCTCAAAATTGTGACTTTAAAACTCAGAATTCCAatttaaaaactcagaattgagaatttataactcagaattgtgacttaatagctcagaattctgacttaataactcagaattgtgactttataactcaaaattctgacttaaatttttttttacgttgtatttatttatttatttattttattcagtggcGGGCTTCCATGGAAACTGCTTTTTCTTGAAAAACACACCTCAGTAAATGAAATCTGTCTGATATGCGGTATTGATATTGGGGTTGCTTAATAATCACTATCATAAAGTCTTTTGTTTTTGCAGTCAATGATTATTTACGACTTTAATTCTACTGTGGTGAAAATAAGGAAGCTTAAACTCTTCAGAGAGTCAGGGAATGTACTTTATGTTTTTTAGTAAAAGCTTTTTAAACATGCAGAtgcagcacaatcgccttacgTCCTCAATGTGAACGTGTACATAATGTAAATATCTGTACTATTGCATTTGTAAGAATTACAGTACTGTATATAgcgaaatgtttatttattgttttttttttgcaatctaaATCTTCATTTGATAATCGGCTTTGTGCCATGTCCGTTGTTTAATTGTTGAATGTAAATGATCATGTTTCTGTACATTCCGATGAGCTAATTTAGTTATGTGTCTTCTGAAAAGCCAAATGCAGTTCTAATAACTTGTGTTATTTTatcttgaaataaaaatatac

Function

GO:

id name namespace
GO:0090118 receptor-mediated endocytosis involved in cholesterol transport biological_process
GO:0042632 cholesterol homeostasis biological_process
GO:0071222 cellular response to lipopolysaccharide biological_process
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0005509 calcium ion binding molecular_function
GO:0005041 low-density lipoprotein particle receptor activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-031217-1 Enables low-density lipoprotein particle receptor activity. Acts upstream of or within cellular response to lipopolysaccharide; cholesterol homeostasis; and receptor-mediated endocytosis involved in cholesterol transport. Predicted to be located in membrane. Predicted to be integral component of membrane. Is expressed in intestine and liver. Human ortholog(s) of this gene implicated in Alzheimer's disease; arteriosclerosis; familial hypercholesterolemia; hepatitis C; and migraine without aura. Orthologous to human LDLR (low density lipoprotein receptor).

Ensembl:

ensembl_id ENSDART00000146955

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00049829 lncRNA upstream 510824 18771528 ~ 18788485 (+) True XLOC_025229
TCONS_00052636 lncRNA upstream 627018 18670824 ~ 18672291 (+) True XLOC_025227
TCONS_00049812 lncRNA upstream 899466 18399317 ~ 18399843 (+) True XLOC_025220
TCONS_00052635 lncRNA upstream 1102183 18189609 ~ 18197126 (+) False XLOC_025218
TCONS_00049852 lncRNA downstream 12836 19336525 ~ 19341041 (+) False XLOC_025242
TCONS_00049856 lncRNA downstream 32244 19355933 ~ 19360577 (+) True XLOC_025244
TCONS_00052334 lncRNA downstream 149274 19472963 ~ 19473197 (+) True XLOC_025248
TCONS_00049864 lncRNA downstream 341651 19665340 ~ 19677031 (+) True XLOC_025251
TCONS_00052637 lncRNA downstream 735989 20059678 ~ 20064732 (+) False XLOC_025257
TCONS_00049847 mRNA upstream 16784 19248973 ~ 19282525 (+) True XLOC_025239
TCONS_00049846 mRNA upstream 17431 19245804 ~ 19281878 (+) False XLOC_025239
TCONS_00049845 mRNA upstream 60915 19216567 ~ 19238394 (+) True XLOC_025238
TCONS_00049844 mRNA upstream 88672 19207176 ~ 19210637 (+) True XLOC_025237
TCONS_00049841 mRNA upstream 331656 18936009 ~ 18967653 (+) False XLOC_025236
TCONS_00049851 mRNA downstream 12597 19336286 ~ 19355200 (+) False XLOC_025242
TCONS_00049855 mRNA downstream 32180 19355869 ~ 19363981 (+) False XLOC_025244
TCONS_00049857 mRNA downstream 123308 19446997 ~ 19457773 (+) True XLOC_025245
TCONS_00049858 mRNA downstream 137302 19460991 ~ 19466015 (+) True XLOC_025246
TCONS_00049859 mRNA downstream 145088 19468777 ~ 19477473 (+) True XLOC_025247
TCONS_00049840 other upstream 331864 18936006 ~ 18967445 (+) False XLOC_025236
TCONS_00049843 other upstream 357595 18936080 ~ 18941714 (+) True XLOC_025236
TCONS_00049842 other upstream 359609 18936046 ~ 18939700 (+) False XLOC_025236
TCONS_00049839 other upstream 381726 18917461 ~ 18917583 (+) True XLOC_025235
TCONS_00049838 other upstream 406543 18892650 ~ 18892766 (+) True XLOC_025234
TCONS_00049853 other downstream 25749 19349438 ~ 19354938 (+) True XLOC_025242
TCONS_00049854 other downstream 26030 19349719 ~ 19349817 (+) True XLOC_025243
TCONS_00049874 other downstream 1356234 20679923 ~ 20680038 (+) True XLOC_025262
TCONS_00049876 other downstream 1701464 21025153 ~ 21030871 (+) False XLOC_025264
TCONS_00049877 other downstream 1701464 21025153 ~ 21030873 (+) True XLOC_025264

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000034_04392399_04400096.mRNA True 2850 mRNA 0.48 17 CI01000034 4392200 ~ 4400096 (-)
rainbow trout (Oncorhynchus mykiss) TU512060 True 634 TUCP 0.52 6 NC_048569.1 87774222 ~ 87805865 (-)