RNA id: TCONS_00027844


Basic Information

Item Value
RNA id TCONS_00027844
length 1953
lncRNA type retained_intron
GC content 0.41
exon number 4
gene id XLOC_013940
representative True

Chromosome Information

Item Value
chromosome id NC_007130.7
NCBI id CM002903.2
chromosome length 48449771
location 13410903 ~ 13420490 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GTAAGTATgttgtttggtgaaatattttgAGTTCTTGAAGAACTAATCTGtccgttaaagggatagttcaccccaaaataattctgcaatcatttactcaccctattgtcattttgagacttttggagaaaaaaaaaaaacatctcaacaGACATCTCAGCAAATCTCTCTTTTTGTGTTGCACAGATGCCATtcgggtgagtaaatgatgacaggatttcaTGTTTATGTGAACTGTCCCTCTAAGTTATAGGGCAAAATTTAATCTGTAATTAATTGTACGCTAGTATAAGAACATCtgtatttaccatttaaaaaacaacaacttttctttcatttttccttGTTTATAGTTAAATCATTGTTTTTGAATAAGGCTAGTTTTAAGACTGTTGTCTTTTATCTGTCCTGAACTGTATGCATCTTATTCTCATCACTTTGAAGGTAATCGCtatggtcgtggtggtggaggaggaggaggggacaGGTACGGCCCACCGACACGCACAGATTACAGGCTGATTGTGGAAAATCTCTCTAGTCGATGCAGCTGGCAGGACCTGAAGGACTACATGCGTCAGGCTGGTGAGGTGACTTATGCTGACACTAATAAGGGTCGCAAAAATGAAGGGGTGATAGAGTTCAGACAATACTCGGATATGAAAAGAGCCCTGGAGAAGCTTGATGGCACTGAGGTCAATGGAAGAAAGATTCGGCTAATTGAGGACCGGCCTGGTGCCAGACGCCGGCGCTCTTACTCTCGCAGTGCCTccagGTCTCGATCCAGGAGCAGGAGGTCTCGCAGAAGCCGAAGCCACAGTCGAACCAGTAGCCGCTCTGGAGCCTCAGGTTCACGATCACGCAGCAGGTCAACCAGCAAGAAGGCTAAGAGCAGGAGCAGCAGGATGGAGGAGAGCAGTAACGGAGCTCGCAAGGGTGGTGATAGCGGCAGGGATAATAGCTTGAGCCGCAGCCCTCAAAATAAAAAGAGCAAACGTGAGAACAAGCGGGGTCGCTCTGATTCTCGGTCCAGATCTCGATCCAAATCGAGGAACGATAGGGATCTGTCCAGAGAGTCTGGGTCCAAATCTCAGGAGGCGAGCAAGAGTGGTGATGAAGGCAGAGCGGGAACACATCGTTCTAGAGCTCATTCTCGATCCAGATCACAAACACCACCAAATGCAGATCAGCGGAGGGAATCTAGATCCAGGTCTAGGTCCAGATCCAAATCACGCTCACATTCACGCTCACAGTCTTATTCCCGATCTCGATCCCGTTCGAGGTCTCGGTCCTAAATCCATTTCTGAAAGTCTTTCTCACTCAGTATTATTCATCTTGTTTTCCAGTCTAGCTAAACGTCTTTAAAACAAGAATatgtcttaaatgtttttttttttttacccctttaAATCTTTTTGTCACAATTGTGATAGATGTATGCttaaaacaaaacacagttaTCAACTGATAGGGGtaagaaaataaatagaattcAAGATATATTGTCTGAAAACAAGTCTGAATGTTACATTTGAGAAGCAAAATGGTGTATcttgtttttagatattttgtcCTCGGAAAAAGACAAGAATAGACTGAAAATTATGTTTTGCAGTCAGTGTCTAAATGTTGTTCTGCCCTTCATTTCTTTTTTTGAAGCTacttttttgtagttttgttttatcCTTTGTTGTCAAATAGACAAGCTAGTTATTAGGGAAATTGCCTGCTTATTCACAGTTATTATTTTCTGAAATTGTTAAccttatgttttattttagtagTGTTTTTCTTTGGAAATTGcttgcatatgttttattcataaaGACCGAGCCCTCAGTAGGTGTCCTAACCCTTTGCATTGTATACTTTAGACCTGTACCATAATTGTTGTTATGCTGGGGCAGAGTTTATGGTctttttaaattcagtttctccatgcaaaacaataaa

Function

GO:

id name namespace
GO:0006376 mRNA splice site selection biological_process
GO:0000380 alternative mRNA splicing, via spliceosome biological_process
GO:0000381 regulation of alternative mRNA splicing, via spliceosome biological_process
GO:0045292 mRNA cis splicing, via spliceosome biological_process
GO:0005634 nucleus cellular_component
GO:0016607 nuclear speck cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0003729 mRNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-030131-591 Enables mRNA 3'-UTR binding activity. Predicted to be involved in alternative mRNA splicing, via spliceosome and mRNA splice site selection. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in membrane and nucleus. Predicted to be integral component of membrane. Predicted to be active in nuclear speck. Orthologous to human SRSF4 (serine and arginine rich splicing factor 4).

Ensembl:

ensembl_id ENSDART00000160531

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00029878 lncRNA upstream 165427 13230383 ~ 13249249 (+) True XLOC_013938
TCONS_00027840 lncRNA upstream 294398 13102224 ~ 13120278 (+) True XLOC_013936
TCONS_00029698 lncRNA upstream 299150 13115265 ~ 13115526 (+) True XLOC_013937
TCONS_00027828 lncRNA upstream 994103 12417514 ~ 12420573 (+) True XLOC_013930
TCONS_00029877 lncRNA upstream 1113785 12295450 ~ 12300891 (+) True XLOC_013928
TCONS_00029879 lncRNA downstream 210848 13631325 ~ 13635810 (+) True XLOC_013942
TCONS_00027846 lncRNA downstream 376115 13796592 ~ 13805873 (+) True XLOC_013943
TCONS_00027851 lncRNA downstream 689024 14109501 ~ 14110107 (+) False XLOC_013947
TCONS_00029880 lncRNA downstream 1430340 14850817 ~ 14871231 (+) False XLOC_013953
TCONS_00029881 lncRNA downstream 1605439 15025916 ~ 15027342 (+) True XLOC_013955
TCONS_00027843 mRNA upstream 777 13410916 ~ 13413899 (+) False XLOC_013940
TCONS_00027841 mRNA upstream 17381 13375838 ~ 13397295 (+) True XLOC_013939
TCONS_00027838 mRNA upstream 227854 13099544 ~ 13186822 (+) False XLOC_013936
TCONS_00027839 mRNA upstream 263465 13099566 ~ 13151211 (+) False XLOC_013936
TCONS_00027837 mRNA upstream 293131 13099541 ~ 13121545 (+) False XLOC_013936
TCONS_00027845 mRNA downstream 407 13420884 ~ 13426991 (+) True XLOC_013941
TCONS_00027848 mRNA downstream 574086 13994563 ~ 14035892 (+) True XLOC_013945
TCONS_00027849 mRNA downstream 638872 14059349 ~ 14061987 (+) True XLOC_013946
TCONS_00027850 mRNA downstream 688871 14109348 ~ 14112967 (+) False XLOC_013947
TCONS_00027853 mRNA downstream 693409 14113886 ~ 14127134 (+) False XLOC_013948
TCONS_00027836 other upstream 469710 12944850 ~ 12944966 (+) True XLOC_013935
TCONS_00027817 other upstream 2136147 11278413 ~ 11278529 (+) True XLOC_013922
TCONS_00027800 other upstream 2579055 10832092 ~ 10835621 (+) False XLOC_013912
TCONS_00027788 other upstream 2847190 10567371 ~ 10567486 (+) True XLOC_013906
TCONS_00027758 other upstream 3970798 9443772 ~ 9443878 (+) True XLOC_013889
TCONS_00027847 other downstream 413402 13833879 ~ 13833993 (+) True XLOC_013944
TCONS_00027852 other downstream 690494 14110971 ~ 14112909 (+) True XLOC_013947
TCONS_00027859 other downstream 974402 14394879 ~ 14398687 (+) True XLOC_013950
TCONS_00027862 other downstream 1430356 14850833 ~ 14852304 (+) True XLOC_013953
TCONS_00027879 other downstream 2641349 16061826 ~ 16061961 (+) True XLOC_013963

Expression Profile

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