RNA id: TCONS_00007458


Basic Information

Item Value
RNA id TCONS_00007458
length 733
RNA type mRNA
GC content 0.44
exon number 6
gene id XLOC_003896
representative True

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 6859876 ~ 6868474 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

gatgatgtgtggatgatttACACGgggcataactaagcaacacagcGATCTGTTAAGGAGGAAGTACTCCCGTTATCTTTACTGAAGACGGCACAGAACCACCCGATGCTGGTGGAGTTAAAGAATGGCGAGACATACAACGGCCATCTGGTCAGCTGCGACAACTGGATGAATATAAACTTGAGAGAAGTTATTTGCACTTCACGGGATGGAGATAAGTTTTGGAGGATGCCAGAATGCTACATAAGAGGAAGCACCATTAAATACTTGCGAATCCCTGATGAAATTATAGATATGGTGAAAGAGGAAGTGGTGTCAAAGGGCCGTGGCCGGGGTGGCATGCAGCAGAATAAGCCACAAGGAAAGGGCAGAGGAGGTGGACCTGGAAGAGGCGGCGGACCTGGCAGAGGTGTTTTTGGTGGCCGTGGCAGAGGCATGCAGGGATCTGGCCGTGGACAGCAACAAGACAAAAAGCCTGGAAAACAACAAGTTTGATCATCGACCAGAAAGAACGAGTTTAATTTGAAATGGACGTCCTGGATCTCCGTGAAGATTTTAATTTGGTGATGTTGATTTAAAGATGCTCTTTCATTCGttctaaactgttttattttgtcttcAGTCATTCGGTGCATGTTTTCACATTTCTCTTTTTGTGCTTTAAAACACAACCATGCTGTAAGTTTGACTTGTCTATATGCACTTGTGAATAAACGATTTTTGTTAAATATGG

Function

GO:

id name namespace
GO:0033962 P-body assembly biological_process
GO:0006396 RNA processing biological_process
GO:0006397 mRNA processing biological_process
GO:0000387 spliceosomal snRNP assembly biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0000956 nuclear-transcribed mRNA catabolic process biological_process
GO:0008380 RNA splicing biological_process
GO:0000932 P-body cellular_component
GO:0005634 nucleus cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005688 U6 snRNP cellular_component
GO:0097526 spliceosomal tri-snRNP complex cellular_component
GO:0017070 U6 snRNA binding molecular_function
GO:0003723 RNA binding molecular_function

KEGG:

id description
ko03040 Spliceosome
ko03018 RNA degradation
ko03019 Messenger RNA biogenesis
ko03041 Spliceosome

ZFIN:

id description
ZDB-GENE-040426-1652 Predicted to enable U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to act upstream of or within mRNA splicing, via spliceosome and nuclear-transcribed mRNA catabolic process. Predicted to be located in nucleus. Predicted to be part of U6 snRNP and spliceosomal tri-snRNP complex. Predicted to be active in P-body. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated).

Ensembl:

ensembl_id ENSDART00000168372

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00008754 lncRNA downstream 59938 6792546 ~ 6799938 (-) True XLOC_003895
TCONS_00008753 lncRNA downstream 403576 6455034 ~ 6456300 (-) True XLOC_003893
TCONS_00008752 lncRNA downstream 428528 6429973 ~ 6431348 (-) True XLOC_003891
TCONS_00008751 lncRNA downstream 428744 6429973 ~ 6431132 (-) False XLOC_003891
TCONS_00008750 lncRNA downstream 535319 6316654 ~ 6324557 (-) True XLOC_003887
TCONS_00007460 lncRNA upstream 842 6869316 ~ 6870035 (-) False XLOC_003897
TCONS_00008451 lncRNA upstream 477326 7345800 ~ 7349497 (-) False XLOC_003908
TCONS_00008755 lncRNA upstream 477452 7345926 ~ 7349386 (-) False XLOC_003908
TCONS_00008756 lncRNA upstream 477452 7345926 ~ 7349427 (-) True XLOC_003908
TCONS_00007486 lncRNA upstream 493950 7362424 ~ 7365383 (-) True XLOC_003910
TCONS_00007453 mRNA downstream 407384 6446235 ~ 6452492 (-) False XLOC_003892
TCONS_00007454 mRNA downstream 407407 6446925 ~ 6452469 (-) False XLOC_003892
TCONS_00007455 mRNA downstream 407432 6447421 ~ 6452444 (-) True XLOC_003892
TCONS_00007451 mRNA downstream 430171 6411169 ~ 6429705 (-) True XLOC_003889
TCONS_00007452 mRNA downstream 438959 6417450 ~ 6420917 (-) True XLOC_003890
TCONS_00007459 mRNA upstream 838 6869312 ~ 6880725 (-) False XLOC_003897
TCONS_00007461 mRNA upstream 1213 6869687 ~ 6877973 (-) True XLOC_003897
TCONS_00007462 mRNA upstream 72915 6941389 ~ 6970107 (-) False XLOC_003898
TCONS_00007464 mRNA upstream 76492 6944966 ~ 6974022 (-) True XLOC_003898
TCONS_00007465 mRNA upstream 108794 6977268 ~ 6985463 (-) True XLOC_003899
TCONS_00007456 other downstream 77800 6780708 ~ 6782076 (-) True XLOC_003894
TCONS_00007441 other downstream 653287 6197276 ~ 6206589 (-) False XLOC_003884
TCONS_00007438 other downstream 787810 6071960 ~ 6072066 (-) True XLOC_003881
TCONS_00007400 other downstream 2906039 3953723 ~ 3953837 (-) True XLOC_003853
TCONS_00007330 other downstream 5771361 1069406 ~ 1088515 (-) False XLOC_003806
TCONS_00007463 other upstream 75826 6944300 ~ 6948018 (-) False XLOC_003898
TCONS_00007477 other upstream 247773 7116247 ~ 7116363 (-) True XLOC_003904
TCONS_00007494 other upstream 1242895 8111369 ~ 8126195 (-) True XLOC_003913
TCONS_00007548 other upstream 4457048 11325522 ~ 11331050 (-) False XLOC_003936
TCONS_00007549 other upstream 4462251 11330725 ~ 11331090 (-) True XLOC_003936

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) TU278644 True 892 lncRNA 0.42 2 CI01000057 4455149 ~ 4457859 (+)
tiger barb (Puntius tetrazona) TU278644 True 1032 lncRNA 0.47 3 NW_025048355.1 1536045 ~ 1541873 (+)