RNA id: TCONS_00033163


Basic Information

Item Value
RNA id TCONS_00033163
length 701
lncRNA type retained_intron
GC content 0.53
exon number 5
gene id XLOC_016990
representative True

Chromosome Information

Item Value
chromosome id NC_007113.7
NCBI id CM002886.2
chromosome length 59640629
location 57825432 ~ 57837838 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

TGCAGCGGGAACAGAGGGAAGCGTGATCTGGACGTTGGGGCATTGGTAGTGAATATCTGCAATCATGGATTTCCAGCACAGAGCTGGAGGAAAAACGGGCAGCGGTGGCGTGGCATCGGCGTCCGAGAGTAACCGGGACCGGCGTGAGCGGCTGCGGCAGCTCGCGTTAGAGACCATCGACATCAATAAAGACCCGTACTTCATGAAAAACCACCTTGGCTCCTACGAGTGTAAACTGTGTCTCACGCTGCACAATAATGAGGGGAGTTATCTTGCACACACTCAGGGCAAAAAGCATCAGTCTAACCTagcgAGGAGAGCTGCGAAAGAGGCGAAGGAGGCGCCGGCTCAGCCTGCTCCAGAGAAAGTCAAGGTGGAGGTCAAGAAGTTTGTCAAGATCGGCAGACCCGGTTATAAAGTAACGAAACAGAGGGATCCAGAGATTGGACAGCAGAGTCTGCTTTTCCAGGTAAATCCTGGAGCTTCTGAGTGTGAACTGCGGGTTGTTTTGGTTGATCTGTGCAGGATTGGATCTTTTCTCTTCTTGTGTTGTTCCTCAGATCGATTACCCAGAGATAGCGGAGGGAATCGGGCCACGGCATCGCTTTATGTCAGCGTATGAGCAGAGAATCGAGCCTCCAGACCGGCGCTGGCAGTATCTGCTGTTCGCTGCTGAGCCGTACGAAACCATCGCTTTCAAG

Function

GO:

id name namespace
GO:0000245 spliceosomal complex assembly biological_process
GO:0071013 catalytic step 2 spliceosome cellular_component
GO:0005634 nucleus cellular_component
GO:0005686 U2 snRNP cellular_component
GO:0071004 U2-type prespliceosome cellular_component
GO:0046872 metal ion binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG:

id description
ko03040 Spliceosome
ko03041 Spliceosome

ZFIN:

id description
ZDB-GENE-040426-897 Predicted to enable nucleic acid binding activity and zinc ion binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U2 snRNP; U2-type prespliceosome; and catalytic step 2 spliceosome. Orthologous to human SF3A2 (splicing factor 3a subunit 2).

Ensembl:

ensembl_id ENSDART00000143973

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00034010 lncRNA downstream 18511 57801654 ~ 57811814 (-) True XLOC_016989
TCONS_00033430 lncRNA downstream 77421 57730336 ~ 57752904 (-) True XLOC_016988
TCONS_00034009 lncRNA downstream 244128 57581671 ~ 57586197 (-) True XLOC_016986
TCONS_00034008 lncRNA downstream 244957 57581671 ~ 57585368 (-) False XLOC_016986
TCONS_00034007 lncRNA downstream 250035 57573353 ~ 57580290 (-) True XLOC_016985
TCONS_00034011 lncRNA upstream 252503 58090321 ~ 58109158 (-) False XLOC_016997
TCONS_00033431 lncRNA upstream 253401 58091219 ~ 58109574 (-) False XLOC_016997
TCONS_00033432 lncRNA upstream 269356 58107174 ~ 58109574 (-) True XLOC_016997
TCONS_00033433 lncRNA upstream 349076 58186894 ~ 58201176 (-) False XLOC_017000
TCONS_00033434 lncRNA upstream 374731 58212549 ~ 58213192 (-) True XLOC_017001
TCONS_00033159 mRNA downstream 123286 57609291 ~ 57707039 (-) True XLOC_016987
TCONS_00033156 mRNA downstream 356334 57447105 ~ 57473991 (-) False XLOC_016984
TCONS_00033157 mRNA downstream 356345 57448301 ~ 57473980 (-) False XLOC_016984
TCONS_00033155 mRNA downstream 361210 57447105 ~ 57469115 (-) False XLOC_016984
TCONS_00033153 mRNA downstream 387115 57416851 ~ 57443210 (-) False XLOC_016982
TCONS_00033164 mRNA upstream 41529 57879347 ~ 57891504 (-) True XLOC_016991
TCONS_00033165 mRNA upstream 54848 57892666 ~ 57900437 (-) False XLOC_016992
TCONS_00033166 mRNA upstream 54849 57892667 ~ 57916317 (-) False XLOC_016992
TCONS_00033167 mRNA upstream 61102 57898920 ~ 57900430 (-) False XLOC_016992
TCONS_00033168 mRNA upstream 75672 57913490 ~ 57918314 (-) True XLOC_016992
TCONS_00033146 other downstream 543067 57268782 ~ 57287258 (-) False XLOC_016979
TCONS_00033145 other downstream 561167 57268781 ~ 57269158 (-) False XLOC_016979
TCONS_00033137 other downstream 726840 57103401 ~ 57103485 (-) True XLOC_016974
TCONS_00033134 other downstream 768532 57058078 ~ 57061793 (-) True XLOC_016972
TCONS_00033120 other downstream 1787695 56042512 ~ 56042630 (-) True XLOC_016962
TCONS_00033170 other upstream 102862 57940680 ~ 57941863 (-) True XLOC_016993
TCONS_00033188 other upstream 798858 58636676 ~ 58636792 (-) True XLOC_017010
TCONS_00033190 other upstream 1030291 58868109 ~ 58869453 (-) True XLOC_017015
TCONS_00033196 other upstream 1200377 59038195 ~ 59038312 (-) True XLOC_017019
TCONS_00033197 other upstream 1264351 59102169 ~ 59102252 (-) True XLOC_017022

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) TU328564 True 1422 lncRNA 0.38 3 CI01000077 321691 ~ 323712 (+)