RNA id: TCONS_00023998


Basic Information

Item Value
RNA id TCONS_00023998
length 2465
RNA type mRNA
GC content 0.50
exon number 11
gene id XLOC_012177
representative True

Chromosome Information

Item Value
chromosome id NC_007128.7
NCBI id CM002901.2
chromosome length 53461100
location 29227502 ~ 29249258 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GGCTTCTCTACCTTTTCGTGCACCTCAACCGAGCCCATTTCAGAACATTCCGATGTCAAAATGACCCGATTTGATCCGACGGCCGTTGTAGCCTGTTTGAGAAGCGAGGACGCAGCCGTGGCCGCGTAAATTTGGACGTTGTTGTCTcggtgtgtgtctgtctgtcataTGAGTGGACCATCCGTGGCTCCATTCGTGAAATTCTTCAGAGAAACACGGTTGGAACATCGGACGACATCGCTGACCAACTGATTCATGTCATGTCCGCAGGGCGTAATGTGGAACAGCAGATTCCCCTGCAGCAGCGTCCTCCATCTCTTGCCATGCCCTCCATGGCCCAGCGGCCCAGGCCCGAGCCAGGCTTCTCTCCCCTGCACGGCGGTTTCCGGGACCACTTTGTCACGACGCCTGAGCCCAAGTATTGCTGTGAGACCTGCAGGCTAGTGCTCTGTAACCCACGCCAGACTGAGTGTGGACATCGCTTCTGTGAAAGCTGCATCAATGAACTGCTCAGTAAGCCTAACCCAGTGTGTCCAGCTGATCTACTACCACTTTTTGAAGATAAGATATTCCGGGATGTTTGCTGCAATAGGGAAATCATGGCTCTTAAGGTCTACTGCCGAAGTGAGAAAAATGGATGTAAAGAACAAATGTGTTTACAGCAGGTCATGGAGCATTTGGTAATTTGTCCATATTTCGAGGTGCCGTGTCCTTTGGGAAAGTGTAAGGAGAAGATGATGAGGAAAGATATGCCCGAGCACCTAAGCCGCAAATGCAAACACCGAGAGGTCACCTGTGAATTCTGCAGTCTCAAAATGGCCCTCACTGAATTACAGAAACACAAAGAAACCGTCTGTCCTGCATTTCCTGTAGCATGTCCTAATCATTGCTCGTTTTCTTCTATTCTAAGAAGTGAGCTGTCAAGTCACCAGCATGACTGTCCAAAGGCTCAGGTGACCTGTTCCTTCATTCGCTACGGATGCTCCTACAAGGGGCTGAATCAAGAGATGAGGGAGCATGAGTCCAGTTTTGCATCTGAGCATCTAAGAATGATGGCAGTCAGAAACACCACACTAGAAGCCAAGgtTGAAGATGTGAAGAGTGAGTTGATGGAGCGTTATAAAGTTCTGCCGAGTCTCAGCAGTCGTCTTGCTGAGGTGGAGCGTCAGTATGAGGAGATGAGAGAAAAGAACAGGCAGCTGGAGCAGAAGCTGGTCAGCATGCAGatGTTGATGAGCTCTCACTCAGAGAAGCTGCTGGAGGTGGAGATGGAGCTGCGGGAGCTCCGTCCACTGCGGGCCATGAGGGAGGAGGTGGAGACTCTCAGGGGCTCTGTGGAGAGCATGCGCTCGATGGTCTCTTCTCTTGACTCAAGCTGTGTCAATTCTGCTTCTGGTTCTCATACCCTGGCCTCCTTAGAGCAGCAGCTCACACGCCATGATGACCTGATGAGCGTTCACGACGTGCGGCTGGCAGAGATGGATCTGAAGCTGCAGGTGCTGGAGACGGCCAGCTTCAATGGTACTCTCATTTGGAAGATTCGGGATTACAAAAGGCGGAAACAGGAAGCTGTGGTCTCCAAAACCCTTTCGCTCTACAGCCAGCCCTTTTACACAGGGTATTTCGGCTATAAGATGTGCGCCCGCGTCTATCTCAATGGAGATGGGATGGGCAAAGGCACACATCTCTCGCTCTTCTTCGTGGTCATGCGTGGTGAATATGATGCCTTGCTACAATGGCCGTTTAAACAGAAAGTAACATTAATGCTAATGGACCAGGGGCCGGCAAGAAAACACTTAGGCGATGCCTTTAAACCGGACCCCAGTAGCAGTAGCTTTCGCCGGCCCACTGGCGAAATGAACATCGCATCAGGCTGTCCGCTTTTTGTGGCTCAGACTGTGCTAGAAAATGGAACCTATATCAAAGACGACACCATCTTTATAAAAGTGACTGTAGACACTTCAGACCTCCCTGACCCTTGAGTTCAACTTCAGCGGGTCCAACTAAAATCAAGAGTCACGCAGAGCCCCTTCCAGCCAAGACTTCAGAGGGCGATGCTGAACAAGGAGCATCCCACAAGTGTGGGGTTCTAACAGACCAAATCAGGAGTTTGGGCTCGTGTGATGGCGTGCTCTTCTGGAAACAACAGTGCCTTGCTGGGCTAGATGGTTACAGCCTTTAAGAGGAGCACAGAGTAGACGAAATCTCCCAAGTCAACCACATCTCAAATGCAGCGAAGAGTAAGACGTCAACTCTAATCCAAGAGACATTCTCGAGGAAAAACAAAAGTGAATGGTTACTAGATCAGATTCCCAACCtcgttcctggaggcacaccgaCAGTACACATTTTAAACTTGTCTGGCTCTTAATCTAATCCGGAAATGTAAGGAAGATGGTGTACTTTTAAGTGTGTGTCCAGTAAAATGGTTGGCACGGTTGATTAACATCCAGCCCAAAGTGAAA

Function

GO:

id name namespace
GO:0045087 innate immune response biological_process
GO:0042981 regulation of apoptotic process biological_process
GO:0070534 protein K63-linked ubiquitination biological_process
GO:0032088 negative regulation of NF-kappaB transcription factor activity biological_process
GO:0046330 positive regulation of JNK cascade biological_process
GO:0033209 tumor necrosis factor-mediated signaling pathway biological_process
GO:0001817 regulation of cytokine production biological_process
GO:0050688 regulation of defense response to virus biological_process
GO:0043122 regulation of I-kappaB kinase/NF-kappaB signaling biological_process
GO:0001878 response to yeast biological_process
GO:0008063 Toll signaling pathway biological_process
GO:0007165 signal transduction biological_process
GO:0009898 cytoplasmic side of plasma membrane cellular_component
GO:0005737 cytoplasm cellular_component
GO:0098802 plasma membrane signaling receptor complex cellular_component
GO:0046872 metal ion binding molecular_function
GO:0004842 ubiquitin-protein transferase activity molecular_function
GO:0005164 tumor necrosis factor receptor binding molecular_function
GO:0031625 ubiquitin protein ligase binding molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG:

id description
ko04064 NF-kappa B signaling pathway
ko04668 TNF signaling pathway
ko04620 Toll-like receptor signaling pathway
ko04621 NOD-like receptor signaling pathway
ko04622 RIG-I-like receptor signaling pathway
ko04657 IL-17 signaling pathway
ko05200 Pathways in cancer
ko05203 Viral carcinogenesis
ko05222 Small cell lung cancer
ko05161 Hepatitis B
ko05160 Hepatitis C
ko05171 Coronavirus disease - COVID-19
ko05164 Influenza A
ko05162 Measles
ko05168 Herpes simplex virus 1 infection
ko05167 Kaposi sarcoma-associated herpesvirus infection
ko05169 Epstein-Barr virus infection
ko05165 Human papillomavirus infection
ko05417 Lipid and atherosclerosis

ZFIN:

id description
ZDB-GENE-040801-257 Predicted to enable tumor necrosis factor receptor binding activity and ubiquitin protein ligase binding activity. Acts upstream of or within response to yeast. Predicted to be located in cytoplasm. Predicted to be active in cytoplasmic side of plasma membrane. Human ortholog(s) of this gene implicated in brain disease. Orthologous to human TRAF3 (TNF receptor associated factor 3).

Ensembl:

ensembl_id ENSDART00000031458

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00024918 lncRNA downstream 6439 29216066 ~ 29221063 (-) False XLOC_012176
TCONS_00024914 lncRNA downstream 204823 28921572 ~ 29022679 (-) False XLOC_012172
TCONS_00024005 lncRNA upstream 472827 29722085 ~ 29723213 (-) True XLOC_012183
TCONS_00024009 lncRNA upstream 726751 29976009 ~ 30054157 (-) True XLOC_012185
TCONS_00024919 lncRNA upstream 828073 30077331 ~ 30082713 (-) True XLOC_012186
TCONS_00024920 lncRNA upstream 902509 30151767 ~ 30225524 (-) False XLOC_012187
TCONS_00024921 lncRNA upstream 954366 30203624 ~ 30225524 (-) True XLOC_012187
TCONS_00023996 mRNA downstream 2594 29216367 ~ 29224908 (-) False XLOC_012176
TCONS_00023995 mRNA downstream 13792 29195962 ~ 29213710 (-) True XLOC_012175
TCONS_00023993 mRNA downstream 33283 29124190 ~ 29194219 (-) False XLOC_012174
TCONS_00023994 mRNA downstream 34515 29124488 ~ 29192987 (-) True XLOC_012174
TCONS_00023992 mRNA downstream 108140 29117027 ~ 29119362 (-) True XLOC_012173
TCONS_00023999 mRNA upstream 2404 29251662 ~ 29271359 (-) True XLOC_012178
TCONS_00024001 mRNA upstream 33605 29282863 ~ 29312506 (-) False XLOC_012180
TCONS_00024002 mRNA upstream 34372 29283630 ~ 29311835 (-) True XLOC_012180
TCONS_00024003 mRNA upstream 127596 29376854 ~ 29771639 (-) False XLOC_012181
TCONS_00024006 mRNA upstream 482895 29732153 ~ 29736019 (-) True XLOC_012181
TCONS_00023997 other downstream 2591 29216367 ~ 29224911 (-) True XLOC_012176
TCONS_00023990 other downstream 415864 28809704 ~ 28811638 (-) True XLOC_012171
TCONS_00023979 other downstream 603326 28624048 ~ 28624176 (-) True XLOC_012165
TCONS_00023977 other downstream 696920 28530467 ~ 28530582 (-) True XLOC_012163
TCONS_00023956 other downstream 1992036 27214891 ~ 27235466 (-) True XLOC_012154
TCONS_00024000 other upstream 23705 29272963 ~ 29273081 (-) True XLOC_012179
TCONS_00024004 other upstream 387947 29637205 ~ 29637321 (-) True XLOC_012182
TCONS_00024011 other upstream 927178 30176436 ~ 30204529 (-) False XLOC_012187
TCONS_00024018 other upstream 1372162 30621420 ~ 30635295 (-) True XLOC_012194
TCONS_00024025 other upstream 1651514 30900772 ~ 30901872 (-) False XLOC_012199

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000189_02080315_02089268.mRNA True 2469 mRNA 0.49 11 CI01000189 2079637 ~ 2089268 (-)
bowfin (Amia calva) TU190947 False 321 TUCP 0.66 2 CM030141.1 20746671 ~ 20747321 (-)
tiger barb (Puntius tetrazona) TU190947 True 1441 lncRNA 0.36 3 NC_056716.1 25392548 ~ 25394247 (-)
mexican tetra (Astyanax mexicanus) TU190947 False 954 lncRNA 0.56 2 NC_035912.1 12378935 ~ 12380551 (-)