RNA id: TCONS_00000395


Basic Information

Item Value
RNA id TCONS_00000395
length 773
lncRNA type retained_intron
GC content 0.48
exon number 4
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

GTAGGCCTGGCCTAAATGTTTTCATCCTTTTCGCTGCCGAAAATGCGCTCGATCGGCCGCCGAACGAAGCTAAAAAATGTCTAAACTGCGATATAAATAGCATTACGCTATCTGAAGGCGCATAGTGAGAGTGTGTGGTTTTTGCGCGACCAGAACGAGCTTCCGCTACGCCTCGAGAGTCATAAGGCCCGCTGACCCATATTCGCGGGAGCGCTCGAGGAAGTGCGCGCATGAAATTCACCATTGCATTTCTTATTATTGCACCACCGTGACTATTCATCGCAGCGCTGCATCGTGATTCACTGACCGAAGGAACTCCGACCTGACCGAGCATCTTTGTGGATGTACGTTCACATTGGCAGGTCCTCTTCACCAATGTCTTCCCAACGTGTGAGGCCTTTTTTATCGCCCGACTGATCCATGAGACCGAGTTATCATGAGCTCCAGAGACAGGGATGATGGCAGTATTTTTGATGGGCTCATGGAGGAAGATGAGAAAGATAAGGCGAAACGAGTTTCGAGGAATAAGTCGGAGAAGAAAAGGCGGGACCAGTTCAACGTCCTCATTAAAGAACTTGGGACCATGCTGCCTGGAAACACACGAAAGATGGACAAGTCTACGATTTTGCAAAAAAGCATAGACTACCTGCGCAAGAACAAAGGTGAGGCAAGAAATCATTTATGTTTTGTTTCACAATGTGTATTATAGCACAATTCAGCAGTCatctagaacagtggttcccaaagtgggcaTCTGAACAATAAGGAGGGGG

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 ENSDART00000144403

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00003061 lncRNA upstream 168037 19253027 ~ 19264970 (+) True XLOC_000239
TCONS_00003060 lncRNA upstream 273722 19113197 ~ 19159285 (+) True XLOC_000238
TCONS_00000388 lncRNA upstream 433461 18965815 ~ 18999546 (+) True XLOC_000235
TCONS_00002827 lncRNA upstream 599564 18829347 ~ 18833443 (+) False XLOC_000233
TCONS_00000397 lncRNA downstream 21303 19458980 ~ 19462463 (+) False XLOC_000242
TCONS_00000398 lncRNA downstream 24248 19461925 ~ 19466220 (+) True XLOC_000242
TCONS_00000412 lncRNA downstream 370764 19808441 ~ 19821195 (+) False XLOC_000250
TCONS_00002828 lncRNA downstream 586255 20023932 ~ 20027926 (+) True XLOC_000253
TCONS_00002829 lncRNA downstream 589212 20026889 ~ 20029066 (+) True XLOC_000254
TCONS_00000393 mRNA upstream 86959 19332837 ~ 19346048 (+) True XLOC_000241
TCONS_00000392 mRNA upstream 101475 19303241 ~ 19331532 (+) True XLOC_000240
TCONS_00000391 mRNA upstream 320073 19094548 ~ 19112934 (+) True XLOC_000237
TCONS_00000389 mRNA upstream 340852 19083501 ~ 19092155 (+) False XLOC_000236
TCONS_00000390 mRNA upstream 342684 19083532 ~ 19090323 (+) True XLOC_000236
TCONS_00000399 mRNA downstream 77551 19515228 ~ 19517791 (+) True XLOC_000243
TCONS_00000401 mRNA downstream 97467 19535144 ~ 19537359 (+) False XLOC_000244
TCONS_00000402 mRNA downstream 100622 19538299 ~ 19561801 (+) True XLOC_000244
TCONS_00000403 mRNA downstream 164712 19602389 ~ 19609673 (+) False XLOC_000245
TCONS_00000405 mRNA downstream 164712 19602389 ~ 19632153 (+) False XLOC_000245
TCONS_00000377 other upstream 1571079 17858380 ~ 17861928 (+) True XLOC_000224
TCONS_00000369 other upstream 1910831 17513515 ~ 17522176 (+) True XLOC_000219
TCONS_00000367 other upstream 2664198 16768683 ~ 16768809 (+) True XLOC_000218
TCONS_00000364 other upstream 2818418 16600698 ~ 16614589 (+) True XLOC_000215
TCONS_00000357 other upstream 2974266 16458525 ~ 16458741 (+) True XLOC_000213
TCONS_00000400 other downstream 97443 19535120 ~ 19539639 (+) False XLOC_000244
TCONS_00000408 other downstream 268022 19705699 ~ 19705832 (+) True XLOC_000247
TCONS_00000413 other downstream 370774 19808451 ~ 19815449 (+) False XLOC_000250
TCONS_00000414 other downstream 377188 19814865 ~ 19819096 (+) True XLOC_000250
TCONS_00000420 other downstream 537914 19975591 ~ 19980987 (+) True XLOC_000252

Expression Profile

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