XLOC_010180 (scn1ba)


Basic Information

Item Value
gene id XLOC_010180
gene name scn1ba
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 41873708 ~ 41897745 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00020173
GGCGTCACATATCTCAAACTCTCTCACTGAACTCCTCATCACAACACTCATCTGCAGGAACAAGAGCAAGCATCCTCAGGATCTGAACTGAACAGTAAAACCCACCATCATCTCCTTTCCCAAACTGTTTAATAAGAGATCCAAAGGACATATTGGATTTGCAATTGATCTGCTGTCTCGTGGACTACTTGCCTCCTTCTCTTTAGTTTGAGTTTgtgagtttgtgagtgtgtgtgtgtttgtgtgtgagtgggAACGACAGAGACTCGACTCTGAAAACAAAGCCTGTGAAGATGTCTGCACTGCGGCTTCTGTGGGTCCCTGCGCTGTTGTGTTTAACACATGCTTGGCTCTGCTATGGAGCGTGTGTGGAGGTCGACTCTGACACAGAGGCAGTGGCGGGAAAAGGCTTCAAACTGACCTGCATCTCTTGCAAGATGAGAGGAGAAGTGGTTGCCTCCGCCACGGTGGACTGGTGGTTCATGGCCAAAGGCGAGAGTGAATTCACACACATCTACACTTATGCAGAAATGACAGCCAGCATAACAGACGAGCGCTTTGAAGACCGCCTGGCCTGGAATGGCAGTAAAAAAACAGACGACGTGCAGGACGGCTCAATTTACATCCTCAACGTCACCTTCAATGACACCGGCACCTTTCGATGCTTCTTCGACAGAATCCTCATCTTCCCCAACTATGAGTACCACACCAACGCCACAAAGTTCATCACCATCAGCGTAGTAGGACATGCAACCCGAGGGATGGCGTCAATCTTGTCTGAGGTGATGATGTACGTGTCCATTATCGGGCTGCAGTTGTGGCTGGTGGTGGAGATGGTTTACTGCTACAGGAAGATTGCAGCAGCCGGAGAGGAAGCGCTGAGAGAGAGCGAGGCGGAATATTTAGCTATAACCTCTGAGAGCAAAGATAACTGTGCAGGTGTAGCGGTGGCAGAATAACACAGgTCTAAAAAAAGCCTCAAGCCAAAAGCTTGAAGCTCTGTCCATCATGACACGACCAACGGCCTCTCCGTCTCCCTCTCTGGCGCTCTGCCAAACCACAGGACCATTGTTTGACCTTTGAGTTCGACTGTGACAGAGGCACCATTATAAACCATCAGGGAAACACAGTCACACATTACGTTAAAGGAAGTGTTTTGTTTTAAGGCACATGATGACCGCTCTGAGTTTAAATGAAGAATGCAGTAATTGTAGCACTGCACATAACAAATCATACCCAACATGACTTGTACATATGTTTTAGCTCTTAACACCTGTAATGCTTTTTCACATCAAGAGAACTCCGCTTTAAATGGGATCAACATAAGTCACTAATATATATCGACTGAGCCAGAGGACTTTAGACATGTTAGAAACTGTGTAGTTCACTAGTATATTTACTGAGCCAGAACAGAAAAGAATATATACACAACTATATACAgatgat
>TCONS_00020174
GTTTAATAAGAGATCCAAAGGACATATTGGATTTGCAATTGATCTGCTGTCTCGTGGACTACTTGCCTCCTTCTCTTTAGTTTGAGTTTgtgagtttgtgagtgtgtgtgtgtttgtgtgtgagtgggAACGACAGAGACTCGACTCTGAAAACAAAGCCTGTGAAGATGTCTGCACTGCGGCTTCTGTGGGTCCCTGCGCTGTTGTGTTTAACACATGCTTGGCTCTGCTATGGAGCGTGTGTGGAGGTCGACTCTGACACAGAGGCAGTGGCGGGAAAAGGCTTCAAACTGACCTGCATCTCTTGCAAGATGAGAGGAGAAGTGGTTGCCTCCGCCACGGTGGACTGGTGGTTCATGGCCAAAGGCGAGAGTGAATTCACACACGTGAGTATGAGACAAAGAACAGGCAATGCAGCTTCATGTGACAGAGACACAGATGCTGCCTTtttccaccacacacacacacaaacacacacacacacacacatcatggaTTACCTAAATTAATGTGCAGTTGCTCAaatcctttttaaaattaaatttaaaagtgaatttaaaacacattaaaagtgcagcttaaagggattgttcaccca
>TCONS_00020175
GTTTAATAAGAGATCCAAAGGACATATTGGATTTGCAATTGATCTGCTGTCTCGTGGACTACTTGCCTCCTTCTCTTTAGTTTGAGTTTgtgagtttgtgagtgtgtgtgtgtttgtgtgtgagtgggAACGACAGAGACTCGACTCTGAAAACAAAGCCTGTGAAGATGTCTGCACTGCGGCTTCTGTGGGTCCCTGCGCTGTTGTGTTTAACACATGCTTGGCTCTGCTATGGAGCGTGTGTGGAGGTCGACTCTGACACAGAGGCAGTGGCGGGAAAAGGCTTCAAACTGACCTGCATCTCTTGCAAGATGAGAGGAGAAGTGGTTGCCTCCGCCACGGTGGACTGGTGGTTCATGGCCAAAGGCGAGAGTGAATTCACACACATCTACACTTATGCAGAAATGACAGCCAGCATAACAGACGAGCGCTTTGAAGACCGCCTGGCCTGGAATGGCAGTAAAAAAACAGACGACGTGCAGGACGGCTCAATTTACATCCTCAACGTCACCTTCAATGACACCGGCACCTTTCGATGCTTCTTCGACAGAATCCTCATCTTCCCCAACTATGAGTACCACACCAACGCCACAAAGTTCATCACCATCAGCGTAGTAGGACATGCAACCCGAGGGATGGCGTCAATCTTGTCTGAGGTGATGATGTACGTGTCCATTATCGGGCTGCAGTTGTGGCTGGTGGTGGAGATGGTTTACTGCTACAGGAAGATTGCAGCAGCCGGAGAGGAAGCGCTGAGAGAGAGCGAGTGAGCACATGATGACCGCTCTGAGTTTAAATGAAGAATGCAGTAATTGTAGCACTGCACATAACAAATCATACCCAACATGACTTGTACATATGTTTTAGCTCTTAACACCTGTAATGCTTTTTCACATCAAGAGAACTCCGCTTTAAATGGGATCAACATAAGTCACTAATATATATCGACTGAGCCAGAGGACTTTAGACATGTTAGAAACTGTGTAGTTCACTAGTATATTTACTGAGCCAGAACAGAAAAGAATATATACACAACTATATACAgatgatc
>TCONS_00020176
GTTTAATAAGAGATCCAAAGGACATATTGGATTTGCAATTGATCTGCTGTCTCGTGGACTACTTGCCTCCTTCTCTTTAGTTTGAGTTTgtgagtttgtgagtgtgtgtgtgtttgtgtgtgagtgggAACGACAGAGACTCGACTCTGAAAACAAAGCCTGTGAAGATGTCTGCACTGCGGCTTCTGTGGGTCCCTGCGCTGTTGTGTTTAACACATGCTTGGCTCTGCTATGGAGCGTGTGTGGAGGTCGACTCTGACACAGAGGCAGTGGCGGGAAAAGGCTTCAAACTGACCTGCATCTCTTGCAAGATGAGAGGAGAAGTGGTTGCCTCCGCCACGGTGGACTGGTGGTTCATGGCCAAAGGCGAGAGTGAATTCACACACATCTACACTTATGCAGAAATGACAGCCAGCATAACAGACGAGCGCTTTGAAGACCGCCTGGCCTGGAATGGCAGTAAAAAAACAGACGACGTGCAGGACGGCTCAATTTACATCCTCAACGTCACCTTCAATGACACCGGCACCTTTCGATGCTTCTTCGACAGAATCCTCATCTTCCCCAACTATGAGTACCACACCAACGCCACAAAGTTCATCACCATCAGCGTAGTAGGACATGCAACCCGAGGGATGGCGTCAATCTTGTCTGAGGTGATGATGTACGTGTCCATTATCGGGCTGCAGTTGTGGCTGGTGGTGGAGATGGTTTACTGCTACAGGAAGATTGCAGCAGCCGGAGAGGAAGCGCTGAGAGAGAGCGAgTCTAAAAAAAGCCTCAAGCCAAAAGCTTGAAGCTCTGTCCATCATGACACGACCAACGGCCTCTCCGTCTCCCTCTCTGGCGCTCTGCCAAACCACAGGACCATTGTTTGACCTTTGAGTTCGACTGTGACAGAGGCACCATTATAAACCATCAGGGAAACACAGTCACACATTACGTTAAAGGAAGTGTTTTGTTTTAAGGCACATGATGACCGCTCTGAGTTTAAATGAAGAATGCAGTAATTGTAGCACTGCACATAACAAATCATACCCAACATGACTTGTACATATGTTTTAGCTCTTAACACCTGTAATGCTTTTTCACATCAAGAGAACTCCGCTTTAAATGGGATCAACATAAGTCACTAATATATATCGACTGAGCCAGAGGACTTTAGACATGTTAGAAACTGTGTAGTTCACTAGTATATTTACTGAGCCAGAACAGAAAAGAATATATACACAACTATATACAgatgatctaaaaaaaaaaaacttgaaatatgTGAACACACATCTATATATCCTTATTTAAAAGATCAAAAACACATGAAAGGGAAGAAATAGCTAGAAAATCAGAACACATTGATGTAcagtattaggggtgtaacgTAATACACATTCGCAACAGAAGCTTGTGTACCCAA
>TCONS_00020177
ATGTCTGCACTGCGGCTTCTGTGGGTCCCTGCGCTGTTGTGTTTAACACATGCTTGGCTCTGCTATGGAGCGTGTGTGGAGGTCGACTCTGACACAGAGGCAGTGGCGGGAAAAGGCTTCAAACTGACCTGCATCTCTTGCAAGATGAGAGGAGAAGTGGTTGCCTCCGCCACGGTGGACTGGTGGTTCATGGCCAAAGGCGAGAGTGAATTCACACACGTGAGTATGAGACAAAGAACAGGCAATGCAGCTTCATGTGACAGAGACACAGATGCTGCCTTtttccaccaccacacacacatcatggaTTACCTAAATTAA

Function

symbol description
scn1ba Contributes to voltage-gated sodium channel activity. Acts upstream of or within sodium ion transport. Predicted to be integral component of plasma membrane. Predicted to be part of voltage-gated sodium channel complex. Is expressed in gill; heart; liver; musculature system; and nervous system. Human ortholog(s) of this gene implicated in Brugada syndrome 5; developmental and epileptic encephalopathy 52; familial atrial fibrillation; and generalized epilepsy with febrile seizures plus 1. Orthologous to human SCN1B (sodium voltage-gated channel beta subunit 1).

GO:

id name namespace
GO:0086091 regulation of heart rate by cardiac conduction biological_process
GO:0086002 cardiac muscle cell action potential involved in contraction biological_process
GO:0006811 ion transport biological_process
GO:0006814 sodium ion transport biological_process
GO:2000649 regulation of sodium ion transmembrane transporter activity biological_process
GO:0001518 voltage-gated sodium channel complex cellular_component
GO:0005887 integral component of plasma membrane cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0017080 sodium channel regulator activity molecular_function
GO:0019871 sodium channel inhibitor activity molecular_function
GO:0005248 voltage-gated sodium channel activity molecular_function
GO:0044325 ion channel binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-060503-604 Contributes to voltage-gated sodium channel activity. Acts upstream of or within sodium ion transport. Predicted to be integral component of plasma membrane. Predicted to be part of voltage-gated sodium channel complex. Is expressed in gill; heart; liver; musculature system; and nervous system. Human ortholog(s) of this gene implicated in Brugada syndrome 5; developmental and epileptic encephalopathy 52; familial atrial fibrillation; and generalized epilepsy with febrile seizures plus 1. Orthologous to human SCN1B (sodium voltage-gated channel beta subunit 1).

Ensembl:

ensembl_id ENSDARG00000060222

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00020173 False 1446 mRNA 0.46 6 41873708 41897579
TCONS_00020174 False 598 lncRNA 0.45 2 41873834 41889297
TCONS_00020175 False 1051 mRNA 0.46 5 41873834 41897580
TCONS_00020176 False 1414 mRNA 0.45 5 41873834 41897745
TCONS_00020177 True 321 mRNA 0.51 3 41874001 41889208

Neighbor

gene id symbol gene type direction distance location
XLOC_010179 si:dkey-199f5.6 coding upstream 34635 41826584 ~ 41839073 (+)
XLOC_010178 mtdhb coding upstream 141249 41717313 ~ 41732459 (+)
XLOC_010177 ubxn11 coding upstream 191962 41668474 ~ 41681746 (+)
XLOC_010176 aste1a coding upstream 293893 41570653 ~ 41579815 (+)
XLOC_010175 BX005012.2 coding upstream 325271 41546763 ~ 41548437 (+)
XLOC_010181 si:ch211-225p5.8 coding downstream 76693 41974438 ~ 41984133 (+)
XLOC_010182 fli1b coding downstream 120296 42018041 ~ 42046881 (+)
XLOC_010183 BX649388.2 coding downstream 168837 42066582 ~ 42073705 (+)
XLOC_010184 NA coding downstream 192561 42090306 ~ 42096260 (+)
XLOC_010185 CU104741.1 coding downstream 372754 42270499 ~ 42308680 (+)
XLOC_010173 BX005012.4 non-coding upstream 400390 41465511 ~ 41473318 (+)
XLOC_010170 NA non-coding upstream 725545 41142659 ~ 41148163 (+)
XLOC_010168 NA non-coding upstream 744388 41129064 ~ 41129320 (+)
XLOC_010166 NA non-coding upstream 819056 41036647 ~ 41054652 (+)
XLOC_010186 NA non-coding downstream 439500 42337245 ~ 42337549 (+)
XLOC_010187 NA non-coding downstream 566264 42464009 ~ 42470156 (+)
XLOC_010191 NA non-coding downstream 622961 42520706 ~ 42521936 (+)

Expression


Co-expression Network