RNA id: TCONS_00000397


Basic Information

Item Value
RNA id TCONS_00000397
length 814
lncRNA type retained_intron
GC content 0.48
exon number 3
gene id XLOC_000242
representative False

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 19433004 ~ 19466453 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

AGTTGGAGGAGCACAGAACAACATTTTAGGCATTGGGACTCAGGCTAGCGTTGTAGCGATACAGGGCCAAAATGTGACAAGTACAGCGCACAGCGGATCTGCTCCACAGCAGCAAACACTTCCACAGCAACAGACTCCTCGATCCCTGCAGCAGAATCTACAGAGCTCTTCTGTAACTCAGTGCGGTCCTGTGTATAATACCATGATGATCAGCCAACCTGCCAATGCCAATGTTGTGCAGATACCCAGCAATCTGGCACCGAAAATCAGTCAAGCCAATGCAATTAACAGGTTTCCAGCCGGGCAGCAGTTGGTCACAAAGATTGTGACGGCTCCAATGGCGTGTGGCGCAGTCATGGTGCCCACGTCGATGTTTATGGGTCAGGTGGTGACCGCGTACAGTCCGTTTACACAACAACAGGGTCAGACGCAGACCATAACACTGCAGACGCAGCCCACCGTGCCTGCAGACCAGCAGACTCAGGCTGCCACATTACAGAGTCAACAGCAGGGGGCGACACAGCAGTCAACAAAACAGCAGCAACCCTTTTTACAGGTAACAAAGTTCACACTGTAGTGGGGTTCAGTGACACGTGCATCACTTCCAACAGTAACACCCTGTTCTTAGCACTCGTTTTTATATTTGCCACATCTCAGTTTTGAGCGTAGCAGACGGATGCACTgggtaggcatgggctggtataagattctgacagtatgataaccttggataaaaatatcacggtttgatggtattgtgatcactgctctaaaatatgttctttttaaatgtctaagtaaaaaacaaaagctt

Function

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0032922 circadian regulation of gene expression biological_process
GO:0009648 photoperiodism biological_process
GO:0007623 circadian rhythm biological_process
GO:0009416 response to light stimulus biological_process
GO:0005634 nucleus cellular_component
GO:1990513 CLOCK-BMAL transcription complex cellular_component
GO:0005667 transcription regulator complex cellular_component
GO:0005737 cytoplasm cellular_component
GO:0005515 protein binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:0070888 E-box binding molecular_function
GO:0046983 protein dimerization activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-030408-2 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and E-box binding activity. Acts upstream of or within circadian rhythm and photoperiodism. Predicted to be located in cytoplasm and nucleus. Predicted to be part of CLOCK-BMAL transcription complex. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human CLOCK (clock circadian regulator).

Ensembl:

ensembl_id ENSDART00000133758

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00000395 lncRNA upstream 21303 19433007 ~ 19437677 (+) False XLOC_000242
TCONS_00003061 lncRNA upstream 194010 19253027 ~ 19264970 (+) True XLOC_000239
TCONS_00003060 lncRNA upstream 299695 19113197 ~ 19159285 (+) True XLOC_000238
TCONS_00000388 lncRNA upstream 459434 18965815 ~ 18999546 (+) True XLOC_000235
TCONS_00003058 lncRNA upstream 625537 18829450 ~ 18833443 (+) False XLOC_000233
TCONS_00000412 lncRNA downstream 345978 19808441 ~ 19821195 (+) False XLOC_000250
TCONS_00002828 lncRNA downstream 561469 20023932 ~ 20027926 (+) True XLOC_000253
TCONS_00002829 lncRNA downstream 564426 20026889 ~ 20029066 (+) True XLOC_000254
TCONS_00003062 lncRNA downstream 683942 20146405 ~ 20147549 (+) True XLOC_000256
TCONS_00003063 lncRNA downstream 1474262 20936725 ~ 20938443 (+) True XLOC_000259
TCONS_00000393 mRNA upstream 112932 19332837 ~ 19346048 (+) True XLOC_000241
TCONS_00000392 mRNA upstream 127448 19303241 ~ 19331532 (+) True XLOC_000240
TCONS_00000391 mRNA upstream 346046 19094548 ~ 19112934 (+) True XLOC_000237
TCONS_00000389 mRNA upstream 366825 19083501 ~ 19092155 (+) False XLOC_000236
TCONS_00000399 mRNA downstream 52765 19515228 ~ 19517791 (+) True XLOC_000243
TCONS_00000401 mRNA downstream 72681 19535144 ~ 19537359 (+) False XLOC_000244
TCONS_00000402 mRNA downstream 75836 19538299 ~ 19561801 (+) True XLOC_000244
TCONS_00000403 mRNA downstream 139926 19602389 ~ 19609673 (+) False XLOC_000245
TCONS_00000405 mRNA downstream 139926 19602389 ~ 19632153 (+) False XLOC_000245
TCONS_00000377 other upstream 1597052 17858380 ~ 17861928 (+) True XLOC_000224
TCONS_00000369 other upstream 1936804 17513515 ~ 17522176 (+) True XLOC_000219
TCONS_00000367 other upstream 2690171 16768683 ~ 16768809 (+) True XLOC_000218
TCONS_00000364 other upstream 2844391 16600698 ~ 16614589 (+) True XLOC_000215
TCONS_00000357 other upstream 3000239 16458525 ~ 16458741 (+) True XLOC_000213
TCONS_00000400 other downstream 72657 19535120 ~ 19539639 (+) False XLOC_000244
TCONS_00000408 other downstream 243236 19705699 ~ 19705832 (+) True XLOC_000247
TCONS_00000413 other downstream 345988 19808451 ~ 19815449 (+) False XLOC_000250
TCONS_00000414 other downstream 352402 19814865 ~ 19819096 (+) True XLOC_000250
TCONS_00000420 other downstream 513128 19975591 ~ 19980987 (+) True XLOC_000252

Expression Profile

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