RNA id: TCONS_00042761


Basic Information

Item Value
RNA id TCONS_00042761
length 4379
RNA type mRNA
GC content 0.43
exon number 25
gene id XLOC_021521
representative True

Chromosome Information

Item Value
chromosome id NC_007134.7
NCBI id CM002907.2
chromosome length 46223584
location 12840080 ~ 12897815 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATGCTTGATTTGGGTGGTTTAACCAGCAGGAGAATGGGAACTTCGTGCATAGGGAACATACCACCATCTTCAttctttgtattatttaattactacTGCATAATCACATTTTACAATTTCAGCATGAATATTTTGTctaaagaaagtttttttttttccttaggaAAATCCAATCTCATGGATGCTATCAGCTTTGTTCTGGCAGAGAAGACCAGCAATTTACGTGTAAAAACGCTAAAGGATTTGATTCATGGAGCTCCTGTGGGAAAACCTGCTGCTAACCGAGCATTTGTGACCATGGTGTACCAGCAGGATGGAGGACAGGAGCTTTCATTTTCCAGAATCATCATAGGTTCCTCTTCAGAGTACCGCATCAATAATAAAGTGGTGGGTCTGTCTGACTACAGTGAGGAACTGGAGAAACTAGGAATCCTCATCAAGGCCAGAAACTTCCTTGTCTTTCAGGGTGCTGTAGAGTCAATTGCAATGAAGAACCCCAAAGAGAGAACAGCTCTGTTTGAAGAGATTTCTCGCTCTGGAGAGCTTGCCCAAGAATATGACAGATGCAAAAAAGAAATGGTCAAGGCTGAAGAGGACACGCAGTTTAACTACCATCGCAAGAAAAACATAGCTGCTGAACGAAAAGAAGCCAAACAGGAAAAAGAGGAGGCAGAGCGTTATCAACGCCTGAAGGATGAGGTGGTGCGAGCTCATGTACAGTTACAGCTGTTTAAACTGTACCACAATGAATCAGAGATTGAGAAACTTAACAGAGAGCTGGCCCACCGCAATAAAGAGATTGATAAAGACAGAAAGCGCATGGACCGTGTGGAGGAAGAGTTAAAAGACAAAAAGAAGGAGCTTGGCAGAATGATGAGAGACCAACAGATGATTGAGAAAGAGATCAAGGAGAAGGATGCAGAACTCAATCAGAAGAGGCCTCTGTACATTAAAGCCAAGGAAAACACTGCCCACAAGATCAAGAAATTGGAAGCTGCCCGTAAATCACTTCAGAATGCACAGAAATGCTACAAAAAGCGCAAGGGAGACATGGATGAGCTGGATCGTGAGCAGGGGGCAGTTGAAATGGCCAGACAGGAGTTTGAGGAGCGGATGGAGGAGGAGGCTCAAAGTCAGGGACAAGATCTACAGCTGGAAGAGAACCAGGTTAAGGCATATCACCGTTTGAAGGAGGAGGCGAGTAAGCGAGCAGCTACCCTGGCTCAAGAGCTAGAGAAATTCAACAGAGACCAGAAAGCTGACCAGGACCGTCTGGACCTGGAGGAGAGGAAGAAAATAGAAACAGAGGCCAAGATCAAGCAAAAAATCAGAGAGATTGAGGAGAACCAAAAACGCATTGAGAAGCTAGAGGACTATATCACTACTAGCAGGCAGTCTTTGGATGAACAGAAAAGAATGGAAGAGGAACTCACAGAAGAAGTAGAACAGGCCAAACGAAGAATAGATGAGATCAACATGGAACTTAACCAGGTGATGGAGCAGCTGGGTGATGCTCGTATCGACAGGCAGGAGAATAGCAGACAACAGCGTAAAGCTGAGATCTTGGAGAGCATCAAGAGGCTGTATCCTGGATCAGTGTACGGGAGACTGATTGACTTGTGCCAGCCTACACAAAAGAAATATCAGATTGCTGTCACTAAAGTGCTGGGCAAAAATATGGATGCCATTATTGTGGATTCTGAAAAGACGGGTCGTGACTGTATCCAATACATAAAAGAGCAGCGTGGTGAACCTGAGACCTTCCTCCCCCTGGACTATCTGGAGGTCAAGCCCACAGATGAGAAGCTACGTGAGCTGCGTGGTGCTAAATTGGTGATTGATGTAATTCGATATGAGCCACCACAGATTAAGAAAGCCCTGCAATATGCTTGTGGAAATGCCCTGGTCTGTGATAATGTGGAGGATGCTCGCAGGATTGCCTTTGGAGGACCATACAGACACAAGACTGTGGCTCTAGATGGGACGTTATTCCAGAAGTCTGGAGTGATCTCTGGTGGTGCCAGTGATCTAAAGGCCAAAGCTCGACGTTGGGATGAAAAAGCTGTTGATAAGCTGAAAGACAGAAAGGAAAAACTCACAGATGAACTTAAAGAACAAATGAAGGCCAAAAGAAAGGAAGCAGAGCTGCGTCAGGTTCAGTCTCAAGCTCATGGTTTGCAGATGAGGCTCAAGTACTCCCAGAGTGATCTGGAGCAAACCAAGACCAGACACCTGTCCCTTAACATGCAGGAAAAATCAAAGCTGGAAAGTGAACTTGCTAACTTTGGTCCACGGATTAATGATATAAAGAGAATCATCCAGTCACGTGAGAGAGATATGAAAGACTTGAAGGACCGCATGAATGTGGTGGAGGATGAGGTGTTTGTTGAGTTCTGTAAAGAGATTGGAGTTCGTAACATTCGTGAATTTGAAGAAGAAAAAGTCAAAAGGCAGAACGAGATTGCAAAGAAACGCTTAGAATTTGAGACTCAAAAAACACGTCTGGCAATACAGCTGGATTATGAGAAAAACCAGCTGAAGGAAGACCAAGAGAAGGTGGTCATGTGGGAACAGACGGTCAAGAAAGATGAAAATGAGATTGAAAAGCTTAAGAAGgaagagCAGAGGAATATGAAGATAATTGATGAGACCATGGCACAATTGCAGGATCTGAAAAACCAGCACTTGACTAAGAAATCTGAGGTTAATGATAAAAACCATGAAATGGAGGAGATCCGCAAGAAACTAGGGGGTGCCAACAAGGAGTTGACGCAGCTGCAGAAGGAAGTGACTGCTATCGAGACCAAGCTGGAGCAAAAACGCAGTGACAGACACAATCTACTGCAGGCTTGTAAGATGCAGGACATCAAACTTCCTCTCCGATCGGGAACTATGGATGACATCAGCCAGGAAgagGGCAATTCACAGGCAGAGGAGAGCCTCAgcagcagtcaaaagacatcgaGCACTGTCTTGGCCAAGGAAGCTCTTATTGAGATTGACTACAACAGCTTGTCTGAGGACTTAAAAGACTCCTTGTCAGATGAGGAGATCAAGGCAGAGATGAACACATTACAGCAAAGACTCAATGAGCAGCAGAGCATCCTGCAAAGGATCAGTGCACCCAACATGAAGGCCATGGAGAAACTAGAGAGTGTCAGAGACAAATTCCAGGAGACCAGCGATGAGTTTGAAGCTGCTAGGAAGAGGGCAAAGAAAGCCAAGCAGGCATTTGAACAGATAAAGAAGGAGAGATTTGACCGTTTCCACGCCTGCTTTGAGTCTGTGGCCACCAACATTGATGAGATTTATAAAGCTCTGTCACGCAACAGCAGTGCCCAGGCATTTCTGGGACCTGAGAACCCAGAGGAGCCATACCTGGATGGTATAAACTATAATTGTGTGGCCCCAGGTAAACGTTTCAGGCCCATGGACAACCTGTCTGGAGGAGAAAAGACTGTGGCAGCTCTAGCCCTACTGTTTGCTATTCACAGCTATAAGCCTGCTCCCTTTTTTGTTCTGGATGAGATTGATGCAGCACTGGATAATACCAACATTGGCAAGGTTGCAAACTACATCAAGGATCAGTCGGTGCAGAACTTTCAGGCTATTGTAATTTCCTTGAAAGAGGAGTTTTACACTAAGGCTGACTCCCTGATTGGAGTTTACCCAGAGCAAGGAGACTGTGTCATCAGTAAAGTTCTGACCTTTGATCTCTCCCAGTATGCAGATGCCAATCCCAATCCAAATGAATGACATGTTTCTGGAAACAACTGTGTTTTGCTCTGTTCTTTCTAAATATCAGCTTGTTTTAGTTCCAAGTTTTCTCTTTAAACTCTTTCTCTGTTCTTCTTTCATTTAGACACGTGATTAGACATTACCTGTGTGTTTTTGGTTTGTGATTTTTGGCAATCATGTGATTTTGATTTAATCCAGACTAATTTGaattgaacatttattttgatgccattacttttaaagttttataGTGTACAACGTTACAATAGAGGCTAAGTAAATGAAGACTTGCAGCAATAATTTCTGTTCATTTGTAAAAGAATTATGTCTTTTGCAGTTACTGCTTTTTAAGTGTGACATTTTAACTAGTTTTCTCTTGAAAAATAAACAACTTTACAGTCATTTGAATACGTGTGAATTTTTTGGATCTTCTACCTTTACCTGCAATTTTGAAATGTCTTATTGGGCTTTAAGGGATTGGTTAGTCGATAAAACTAAGTCAATAAAAAAACTAACTgggttaaaataataattagcaaaaataaatgatGGAAGTTTTGTGGTGTGAAATCTGACCTGCAGCTGCATGGTTTTAGAAACACCTATACATGCGCTTTTACCCACAAACACATTAAGTCAAG

Function

GO:

id name namespace
GO:0051276 chromosome organization biological_process
GO:0007064 mitotic sister chromatid cohesion biological_process
GO:0048703 embryonic viscerocranium morphogenesis biological_process
GO:0006281 DNA repair biological_process
GO:0008278 cohesin complex cellular_component
GO:0005634 nucleus cellular_component
GO:0005694 chromosome cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0005524 ATP binding molecular_function
GO:0003682 chromatin binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040426-57 Predicted to enable DNA binding activity. Acts upstream of or within embryonic viscerocranium morphogenesis. Predicted to be located in chromosome and membrane. Predicted to be integral component of membrane. Predicted to be part of meiotic cohesin complex. Predicted to be active in nucleus. Is expressed in several structures, including cranium; digestive system; nervous system; optic cup; and otic vesicle. Used to study Cornelia de Lange syndrome. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome 2 and developmental and epileptic encephalopathy. Orthologous to human SMC1A (structural maintenance of chromosomes 1A).

Ensembl:

ensembl_id ENSDART00000183015

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00044789 lncRNA upstream 22389 12673403 ~ 12830266 (+) False XLOC_021518
TCONS_00044790 lncRNA upstream 22389 12674050 ~ 12830266 (+) True XLOC_021518
TCONS_00044792 lncRNA upstream 152241 12698971 ~ 12700414 (+) True XLOC_021520
TCONS_00044791 lncRNA upstream 177234 12674927 ~ 12675421 (+) True XLOC_021519
TCONS_00044788 lncRNA upstream 573607 12259536 ~ 12279048 (+) True XLOC_021514
TCONS_00042762 lncRNA downstream 18244 12916059 ~ 12919734 (+) False XLOC_021522
TCONS_00044793 lncRNA downstream 727098 13624913 ~ 13625531 (+) True XLOC_021528
TCONS_00044659 lncRNA downstream 758220 13656035 ~ 13656319 (+) True XLOC_021529
TCONS_00044794 lncRNA downstream 946742 13844557 ~ 13847704 (+) False XLOC_021532
TCONS_00044795 lncRNA downstream 946939 13844754 ~ 13850492 (+) True XLOC_021532
TCONS_00042756 mRNA upstream 239721 12545114 ~ 12612934 (+) False XLOC_021517
TCONS_00042757 mRNA upstream 289809 12545182 ~ 12562846 (+) True XLOC_021517
TCONS_00042753 mRNA upstream 362654 12454542 ~ 12490001 (+) False XLOC_021516
TCONS_00042763 mRNA downstream 18247 12916062 ~ 12934871 (+) True XLOC_021522
TCONS_00042764 mRNA downstream 226270 13124085 ~ 13332863 (+) True XLOC_021523
TCONS_00042765 mRNA downstream 477544 13375359 ~ 13516852 (+) True XLOC_021524
TCONS_00042767 mRNA downstream 630238 13528053 ~ 13600004 (+) False XLOC_021526
TCONS_00042768 mRNA downstream 630735 13528550 ~ 13599156 (+) False XLOC_021526
TCONS_00042749 other upstream 634280 12213967 ~ 12218375 (+) True XLOC_021513
TCONS_00042745 other upstream 701988 12134839 ~ 12150667 (+) False XLOC_021511
TCONS_00042743 other upstream 768984 12083557 ~ 12083671 (+) True XLOC_021510
TCONS_00042741 other upstream 916955 11935584 ~ 11935700 (+) True XLOC_021508
TCONS_00042731 other upstream 2246109 10601324 ~ 10606546 (+) True XLOC_021503
TCONS_00042766 other downstream 544793 13442608 ~ 13442722 (+) True XLOC_021525
TCONS_00042770 other downstream 706403 13604218 ~ 13604320 (+) True XLOC_021527
TCONS_00042779 other downstream 1570188 14468003 ~ 14470571 (+) True XLOC_021539
TCONS_00042786 other downstream 2455318 15353133 ~ 15353249 (+) True XLOC_021542
TCONS_00042789 other downstream 2852203 15750018 ~ 15751546 (+) True XLOC_021546

Expression Profile

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