RNA id: TCONS_00008949


Basic Information

Item Value
RNA id TCONS_00008949
length 3049
RNA type mRNA
GC content 0.48
exon number 8
gene id XLOC_004468
representative True

Chromosome Information

Item Value
chromosome id NC_007123.7
NCBI id CM002896.2
chromosome length 49182954
location 3912544 ~ 3923070 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATTAGAAGACaagaaacacacagagagagaaggGGAAAAGAAGACTTTGAAAGAGATCTCCTCCATTATAGAAGCTCAGTGAAGCTTTGATTTAATATTCGATAAAGACAAACGTGAAGAAAGAGCAGACCGAGACATGCTGGGTGTGGAAATGTACCCTGGTTTGGCTCTGGGACCTCAGAGATTGAGCGACTGCTATTACAGAGATCGAGATGTGCCGTTGTACCCGTCCACATGTGAGATGGCAGCTCGCGCTCTTCCTCCTGCACTGCTAAAGCCTCATGCAAACACAGACTCTCCTGCCACTCCACAGGACAGCGTGAGGATGGAGCTGGAGAACGCGGGTCTGTGGAAGCAGTTCAGCACAGTCGGGACTGAGATGATCGTCACTAAGAAGGGCAGGCGAATGTTTCCTCAGCTGCGGGTGAAGCTATCAGGGCTGAACCCATCTCTGCGCTACATTCTTCTTCTAGACATCGTACCTGTCGATTCCTCCCGCTATCGTTTTCAAGATAACAGCTGGCAGGTGGTCGGAGGAGCAGAGGCTCGACTGCCGGACCGTGTGTTCATCCATCCGGACTCACCGGCGACTGGAGAACACTGGCAGAACCGCACCATATCCTTCCACCGGGCCAAACTCACCAACAACACGCTGGACGCACAAGGATATATCATTCTTCACTCCTTGCATCGATACCAGCCACGGGTGCATGTGATCGAGGCCCGTGATGTGCTGATGTGGGGAAGAACTCAGCACTCTTTCACTTTTCCTGAAACACAGTTCATTACGGTCACTGCATACCAGAACAACAAGATCACCGAACTGAAAATAAACTCAAATCCTTTTGCGAAAGGCTTTAGAGAGAATGGCATGAACTGCAAGAAGCAAAGAGAGGCAAGGCTGAAGAGGAAAATTACATCCAGCCAAGAGGAATGTTTGGATATTGAGTCATGTGACCCATGTGATTCCACGGAGCTCCTCCCACAATCTGTGGATCTCCCAAGCTCCGCCCTCACCATTATGAACACCGCCCTTCCAATTACAGACTCTGGTTTTCATACAGAAGTGTCATCTCACCCAGATCAGACAGACTCTGACCAAACTCTTGTCCTTGAACAAGCCTTCTTGACCTCTGAGATGCCCTCTTCAATGGAGAGTCAACAACAGACAACCTCTGAAACTAACGTAAACAACGCACTGATGGATGAAACCGGTCAAATGATGGACCTTTCTGGATACACATCATCTTTCCCAACTCCTCAGCTCAGCTCGCATACATCAGTGCCTCAGTCTTCTTCAATGTATTCTGTGGTGTCCTCAACGCAGAGCTCAGACCTTGAGCTTCCACAGGCCTCAAGTATTTCATCTCCACACTCTATGCCTGCATATTCCTCTATACCTTCAGCAGAGTATCCTGGCGTAAATTCCTCTACAGCTATGCCTGCATCTACAACCTCTCTCTCAGACTCATACCCTTCTATCTCACACTCCACCTCTTCACACCTTCTCCAATCTTCATCCTACCATTCTCTTCTTCCAACAGACCAATCCCAAGACAACCTAAGCCCCCATACACCTACAAATCCACCTTTCCAATCAATCCCTGCTTGTCAAGGTACCAGGTTGACTATTGACTCTGGCCAAAATCAGGTGGATGATGGAGGTTTGAGCTCAGCCAATGCGACAACTCCTGCAGTCCCAAACCCAACCCAAACAGCCTTTCCTTTCCCTCCGGTGCAACCCAACAATGACCCTGATCCAACATCCCCTTCATGTCAAAGTCTACCCCAGTCTGCCTTACCATATCAGCAAGTGTCACAATGCAACCAAATTCCCACCCCCTCTGATCCAAATACAACTCCAACCGCATTTCCCTTCCCTCCATCAGAACAGTCCACCCCTAACTCTATTATGGTATCTTCCAATCCAAACACAACAGCCTTCCCCTTTCCCCCTGTTCAGCAGCAACTCAACTTGAGTACCTCTGGACCTAGTTCTTTTCCAGTTTCCCAGTCCTCTGGGTTAAACGCAATTCCAAATCCAGTACATCCAACAACTGGATCATTTTCCTTCCCTTCCACCAGTGCTATCCATCAAGGCCCAATGCAGTCTGTTCCCAACACATTGCACCCTAGCACAGCATACACATTCCCTTCATCTCTGCCCAAACACACTGGTCCTCTCCCAAACCCTGCACCAACTTCTTACCCCTTCCCAACTCCAATCCCACCAGGTCCACATCCTCTCCAGAGTTTGACCCTCCCCTCATCCTGCTCAATCCCGAATACATCCCAAATTCAATCCACCTTTCCCCAGTCATACCATAATCCATCCTTCTCTCACATTCCACCCCAAATGGCAAACCACTCTCAAATCACTTCCCAGTCCTTTCCCCCTCTCCAAACCTCAAGTGCCCCCCAGTTACTATCTCAATCCTCAACTCACCCCCAATGTCCTCCTCCTTCAAACGCATACCCTGCCGTAGCTCCAACTGAGATAGGCACCTTCCCACAACTCAACTCTGCCGCCCCCTATCTACCAGATGTGGTACTGCACCCTTCCATACTTCCTTCTCTCGACCCCTCACTCTCCTCCTCTGCTCCGCCATCCCTTTATAACCCATTTCCTTCCTACTCACTACGTCTTTGCCAGGATCCTCGGTCCTCCCTGCATTTACCCCTCAGGCATATTTATAGACAGCCACAACATGCTCATGGTCAGGGCTCTTACTTTGACCTTGGAGGACGAACAGTGTTCTGAAGAGAAACAGAAACATGACAAGCAAGTCAAGAGCTGGCAAGTGACATGTCTGGTGATGGAAGCACTGCATCGGAGGACCTGTGAGACAACAAGAGATGAACCAAAACACTGTAGTTTAAAGTGTAAAATTTTAAAGTAAACCCTGATTCTGCTGTTCTTGAAATAGTTTCAATGCTTTTGTGTGGTTTTATTCAGAGTAATGCTTGATGAAGTTGAATAATGATGTATATTTTTTTCGTATTTCTCTTCATACCCTTGAATtaccaaataaaattttaatgagtttaa

Function

GO:

id name namespace
GO:0021523 somatic motor neuron differentiation biological_process
GO:0001708 cell fate specification biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0001756 somitogenesis biological_process
GO:0048514 blood vessel morphogenesis biological_process
GO:0007275 multicellular organism development biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0048641 regulation of skeletal muscle tissue development biological_process
GO:0061053 somite development biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0001947 heart looping biological_process
GO:0000785 chromatin cellular_component
GO:0005634 nucleus cellular_component
GO:0005515 protein binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function

KEGG:

id description
ko03000 Transcription factors
ko03019 Messenger RNA biogenesis

ZFIN:

id description
ZDB-GENE-020416-5 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including regulation of skeletal muscle tissue development; somatic motor neuron differentiation; and somitogenesis. Located in chromatin. Is expressed in several structures, including margin; mesoderm; presumptive mesoderm; tail bud; and trunk. Human ortholog(s) of this gene implicated in spondylocostal dysostosis. Orthologous to human TBX6 (T-box transcription factor 6).

Ensembl:

ensembl_id ENSDART00000013465

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00010870 lncRNA upstream 892988 2995887 ~ 3019556 (+) False XLOC_004459
TCONS_00008935 lncRNA upstream 903622 3003970 ~ 3008922 (+) True XLOC_004459
TCONS_00010866 lncRNA upstream 1140154 2769589 ~ 2772390 (+) False XLOC_004456
TCONS_00010871 lncRNA downstream 63009 3986079 ~ 3991423 (+) False XLOC_004469
TCONS_00010872 lncRNA downstream 63024 3986094 ~ 3991423 (+) False XLOC_004469
TCONS_00010873 lncRNA downstream 63121 3986191 ~ 3991423 (+) False XLOC_004469
TCONS_00010874 lncRNA downstream 63133 3986203 ~ 3991423 (+) False XLOC_004469
TCONS_00010875 lncRNA downstream 63138 3986208 ~ 3991423 (+) True XLOC_004469
TCONS_00008948 mRNA upstream 2806 3875901 ~ 3909738 (+) True XLOC_004467
TCONS_00008947 mRNA upstream 22328 3871452 ~ 3890216 (+) False XLOC_004467
TCONS_00008945 mRNA upstream 50785 3848109 ~ 3861759 (+) False XLOC_004466
TCONS_00008946 mRNA upstream 51310 3848114 ~ 3861234 (+) True XLOC_004466
TCONS_00008942 mRNA upstream 180530 3723650 ~ 3732014 (+) False XLOC_004465
TCONS_00008950 mRNA downstream 113339 4036409 ~ 4044132 (+) True XLOC_004470
TCONS_00008951 mRNA downstream 191331 4114401 ~ 4145033 (+) False XLOC_004473
TCONS_00008952 mRNA downstream 193446 4116516 ~ 4143661 (+) True XLOC_004473
TCONS_00008953 mRNA downstream 224644 4147714 ~ 4157240 (+) False XLOC_004474
TCONS_00008954 mRNA downstream 226042 4149112 ~ 4157153 (+) True XLOC_004474
TCONS_00008894 other upstream 3390722 509947 ~ 521822 (+) True XLOC_004427
TCONS_00008960 other downstream 574294 4497364 ~ 4497479 (+) True XLOC_004480
TCONS_00008972 other downstream 1128492 5051562 ~ 5051697 (+) True XLOC_004492
TCONS_00008973 other downstream 1129373 5052443 ~ 5052578 (+) True XLOC_004493
TCONS_00008974 other downstream 1134151 5057221 ~ 5057356 (+) True XLOC_004494
TCONS_00008975 other downstream 1138497 5061567 ~ 5061697 (+) True XLOC_004495

Expression Profile

//

Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000047_04105620_04111019.mRNA True 3113 mRNA 0.48 8 CI01000047 4105423 ~ 4111184 (-)