RNA id: TCONS_00002241


Basic Information

Item Value
RNA id TCONS_00002241
length 1237
RNA type mRNA
GC content 0.42
exon number 5
gene id XLOC_001364
representative False

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 38169512 ~ 38171787 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GAGGCGGCCAATGGGAGTTTGAAGCGGCGCCTACAGCTTTGCTGATTCAAATTTGAACCTGTCCCaaccaatcagatgagagctgtgaaGGTGGAGTCTATGGGCATTTAATCAAGTTTGTGCGCGCAGCGACAAAACAGTTTACAACAAGACTACGTACGTTTTGTCGAGCAGTTGAAGCTGAATATAGTCATGGGTAAAGATCCAAATAAGCCCAGAGGGAAAACGTCCTCTTACGCCTTCTTCGTGCAAACCTGCCGGGAGGAACACAAGAAGAAAAACCCAGGGACCTCGGTGAACTTTTCAGAGTTCTCCAAGAAGTGCTCTGAAAGATGGAGGaccatgTCCTCCAAGGAGAAGGGCAAGTTTGAGGAAATGGCTAAGACTGATAAGGTTCGCTATGACCGAGAGATGAAAAACTATGTGCCTCCGAAAGGTGCAAAGGGAGGGAAAAAGAAGAAGGATCCAAATGCACCAAAGAGGCCACCATCTGCTTTCTTTGTCTTCTGCTCTGATCATCGTCCAAAGGTGAAGGGCGACAACCCGGGCATCTCTATTGGTGACATTGCAAAGAAGCTTGGGGAAATGTGGTCCAAGCTTTCACCAAAAGAGAAGTCTCCATATGAGCAGAAGGCCATGAAGCTGAAGGAGAAATATGAAAAGGATGTTGCTGCATATCGCGCCAAAGGTGGAAAACCAGATGGTGCCAAGAAGGGTGGACCTGGCCGGCCAGCAGGAAAGAAGGCAGAAgctgatgatgacgatgatgaggATGAAGATGAGGAGGATGAGGAAGAAGAGGATGAGGAGGACGAGGATGATGATGACGAATAAACTATCAGGAAAACTTGAGCTGAGTTGTTTGCAAAACAATGTGAATGcattttttagcatttaaaaatttAAGACATGTACAGAAATGTGTATAATTGAATACATATGGAGGTCATGTGCTGTTTTGTAAATGtaacagctttattttttttttaaagcactgcTTTTTTTTGTCTGATAGCTGTGGATGCTTTGGTTTCTTTCCCTGTTTCATTATTTCTACTGCCATTTTAAGACTAATGAGGAACAATTTGACTGTAGTGTCTCAATTTTTAAAGCAAGCTTTAAAGTTGTCtagactgaattttttttttctttttttaattttgtatattaTGACTGTTTCCCCTTTTCACTGTGTGCAATTTTGAATTCATTTGACTTATTAAAGGATTTTGCAGAA

Function

GO:

id name namespace
GO:0006310 DNA recombination biological_process
GO:0045089 positive regulation of innate immune response biological_process
GO:0006338 chromatin remodeling biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0008134 transcription factor binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003682 chromatin binding molecular_function
GO:0008301 DNA binding, bending molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-051120-126 Predicted to enable DNA binding activity, bending. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Is expressed in central nervous system; gut; neuromast; ovary; and pectoral fin bud. Orthologous to human HMGB2 (high mobility group box 2).

Ensembl:

ensembl_id ENSDART00000047159

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00003446 lncRNA downstream 1696690 36450821 ~ 36472822 (-) True XLOC_001357
TCONS_00003444 lncRNA downstream 1696700 36424768 ~ 36472812 (-) False XLOC_001357
TCONS_00003443 lncRNA downstream 1696700 36424768 ~ 36472812 (-) False XLOC_001357
TCONS_00003445 lncRNA downstream 1696700 36450821 ~ 36472812 (-) False XLOC_001357
TCONS_00002968 lncRNA downstream 1813046 36355781 ~ 36356466 (-) True XLOC_001356
TCONS_00003447 lncRNA upstream 4075 38175862 ~ 38190204 (-) True XLOC_001365
TCONS_00003448 lncRNA upstream 479373 38651160 ~ 38709154 (-) False XLOC_001370
TCONS_00002255 lncRNA upstream 493380 38665167 ~ 38709221 (-) False XLOC_001370
TCONS_00002254 lncRNA upstream 493380 38665167 ~ 38756904 (-) True XLOC_001370
TCONS_00002263 lncRNA upstream 707418 38879205 ~ 38886725 (-) False XLOC_001372
TCONS_00002240 mRNA downstream 468384 37697381 ~ 37701128 (-) True XLOC_001363
TCONS_00002239 mRNA downstream 468391 37697373 ~ 37701121 (-) False XLOC_001363
TCONS_00002237 mRNA downstream 785771 37379063 ~ 37383741 (-) False XLOC_001362
TCONS_00002236 mRNA downstream 785771 37379063 ~ 37383741 (-) False XLOC_001362
TCONS_00002235 mRNA downstream 785771 37379063 ~ 37383741 (-) False XLOC_001362
TCONS_00002245 mRNA upstream 21360 38193147 ~ 38195012 (-) True XLOC_001366
TCONS_00002246 mRNA upstream 174256 38346043 ~ 38361496 (-) True XLOC_001367
TCONS_00002247 mRNA upstream 226909 38398696 ~ 38415158 (-) True XLOC_001368
TCONS_00002248 mRNA upstream 244319 38416106 ~ 38538284 (-) True XLOC_001369
TCONS_00002249 mRNA upstream 477354 38649141 ~ 38709551 (-) False XLOC_001370
TCONS_00002233 other downstream 805522 37363872 ~ 37363990 (-) True XLOC_001360
TCONS_00002211 other downstream 2834096 35333000 ~ 35335416 (-) True XLOC_001346
TCONS_00002209 other downstream 2834342 35332924 ~ 35335170 (-) False XLOC_001346
TCONS_00002210 other downstream 2834419 35333000 ~ 35335093 (-) False XLOC_001346
TCONS_00002208 other downstream 2851303 35317354 ~ 35318209 (-) True XLOC_001345
TCONS_00002252 other upstream 479373 38651160 ~ 38665973 (-) False XLOC_001370
TCONS_00002253 other upstream 485840 38657627 ~ 38709154 (-) False XLOC_001370
TCONS_00002260 other upstream 636902 38808689 ~ 38813418 (-) False XLOC_001371
TCONS_00002265 other upstream 1202015 39373802 ~ 39373911 (-) True XLOC_001373
TCONS_00002266 other upstream 1503919 39675706 ~ 39677920 (-) True XLOC_001374

Expression Profile

//

Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000049_05514862_05516656.mRNA True 2403 mRNA 0.40 5 CI01000049 5514452 ~ 5518034 (-)
striped catfish (Pangasianodon hypophthalmus) TU47972 True 858 lncRNA 0.47 5 NC_047597.1 3838818 ~ 3840942 (-)
bowfin (Amia calva) TU47972 True 375 lncRNA 0.42 1 CM030125.1 2031837 ~ 2032211 (-)
mexican tetra (Astyanax mexicanus) TU289182 False 1078 lncRNA 0.44 5 NC_035921.1 519212 ~ 528025 (-)