XLOC_025880 (tsen54)


Basic Information

Item Value
gene id XLOC_025880
gene name tsen54
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 60761811 ~ 60795831 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00050747
AGATTAGCAGATTAGTGCTGAAGGAAGCAAAGCTACCGAGTGAGTCTGTGACGCTCTGAAGTCCGTCAGAGCTGTTTGAGGCTCGCTCCCGCAGCCATAAGATCCCAGTGCGTGGCCAGAAAGAGTTCCTGCCCAGCGGCTCCGAGCAGCAGAGCCAACGACTGCAGCACAGCCTGGAGGAGCACTGGACACTGCTGGCTGAGGAGAGAGTCGAGAGACTAGGGAATCTGGTGAATGCAGTATGGAGTCCTGAAGAAAAACTGGTGGAGTTGCAGTCACCGGCTGGGAAGTTTTGGCAGACGATGGGTTTTTCAGAAAGAGGCAAGCAGTATCTGCAACCCGAAGAGGCGCTCTACCTCATGGAATGTGGCAATGTGCAGGTGTTTTACCGGGACCTTCCTCTGTCCATTCAGGACGGATATGAGCGGTTTCTGTCCTCTGACACTGTGACTCTTCATCAGTATCAGGTTTTTGGACATTTGAAAAGGCTTGGGTATGTTGTGAACAGATTTGATCCCAGTTCAGTCTCATCCACATATGAGAGACAGCTGAATCTGCCAGCATCGGACAAACAGAAGAAACAGCTGAAGAGGAAACGCTCTCAAAGTCCTGTGTCCAGTGATAAACACGGCATATCAACAGAGGAGAAGACGACATCTGAAGCTCACAATGAGCTAGCGGAGACCAGTAAACTACCAGCAGATCTGCAGGAGCCGGTACATTTAGCTGACGCACCTGAGAGGACATGGTGGATGGAGGAGGACGTCCAGCAAAAACACCCAAAAACCCAAACTGCAGCTCCCCGTTGGGACTTCAGCAGCATTAGTTTCCCAGATCTGGGCTCCCGCAGGAGATCTGAGCGTTTGGCGTCTCCACACCGCAGCCTGCTGCCGGAAAATGTAGATGTGGGTGAATGTGACGTGTCCCGCTGGCTGGGCAGACTCAACATGAAGCAGGAGAAGCTGTCGCGGCGGGACATGGAGCGACAGAGGGAGCGGGACAGATACCGCAGGGATGTTAACAGTGACCGGGAGGTGCGGCGCTGCAGGAACTGGGCAGAATATTCAGAGCTGATGGAGGAACGGAGGAGGCGGAGGAGAAAACACAGACCTGAACACCTGTGGGAGAGAGAGGAGACGCCGCTCACTCAGCCCGGACAGTGCACATCACACCGTGAACTGCTGGACCAGATCGGCATCATCAAGTCCTCTACTTTCTCTGAGGGTCTTTCCAGATTGTCCCCGTCAGACCAGTGGAAGATTAGTTTCGATGTTTACCAACCAGACACGGTGGCGGAGTTTAAAAAGAGCCACCCTGGAAAGCCTTACACACGCATGTGTGTctgcagtttTGCGGGCCCTGTGCCGGATCTGCATGCTGTGAAGCAGCTCTCCTTCCAGAGCCAGGACGTCCCGGTGACATTCGCAGTGGTGGATCACGGTGACATCTCCTTTTACTGCTTCAAAGACTTTAAACTTCCAACTGATGTGTATTAAAGCTGCATTTATCAAACT

Function

symbol description
tsen54 Acts upstream of or within brain morphogenesis. Predicted to be part of tRNA-intron endonuclease complex. Is expressed in midbrain hindbrain boundary and telencephalon. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2A; pontocerebellar hypoplasia type 4; and pontocerebellar hypoplasia type 5. Orthologous to human TSEN54 (tRNA splicing endonuclease subunit 54).

GO:

id name namespace
GO:0000379 tRNA-type intron splice site recognition and cleavage biological_process
GO:0048854 brain morphogenesis biological_process
GO:0000214 tRNA-intron endonuclease complex cellular_component

KEGG:

id description
ko03016 Transfer RNA biogenesis

ZFIN:

id description
ZDB-GENE-050522-454 Acts upstream of or within brain morphogenesis. Predicted to be part of tRNA-intron endonuclease complex. Is expressed in midbrain hindbrain boundary and telencephalon. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2A; pontocerebellar hypoplasia type 4; and pontocerebellar hypoplasia type 5. Orthologous to human TSEN54 (tRNA splicing endonuclease subunit 54).

Ensembl:

ensembl_id ENSDARG00000036844

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00050747 True 1514 mRNA 0.53 11 60761811 60795831

Neighbor

gene id symbol gene type direction distance location
XLOC_025879 foxj1a coding upstream 28089 60716904 ~ 60733722 (+)
XLOC_025878 NA coding upstream 76841 60677234 ~ 60684970 (+)
XLOC_025877 CABZ01068050.1 coding upstream 113577 60646736 ~ 60648234 (+)
XLOC_025876 mfsd11 coding upstream 137772 60607241 ~ 60624039 (+)
XLOC_025875 mettl23 coding upstream 168832 60589157 ~ 60592979 (+)
XLOC_025881 NA coding downstream 1592 60797423 ~ 60798872 (+)
XLOC_025882 CABZ01087514.1 coding downstream 32982 60828813 ~ 60841194 (+)
XLOC_025883 NA coding downstream 65416 60861247 ~ 60862752 (+)
XLOC_025884 helz coding downstream 161681 60957512 ~ 61034549 (+)
XLOC_025885 NA coding downstream 243242 61039073 ~ 61041115 (+)
XLOC_025429 BX649540.1 misc upstream 30512775 30248739 ~ 30249036 (+)
XLOC_025874 NA non-coding upstream 217672 60543113 ~ 60544139 (+)
XLOC_025873 NA non-coding upstream 322233 60438114 ~ 60439578 (+)
XLOC_025872 NA non-coding upstream 372916 60388249 ~ 60388895 (+)
XLOC_025888 NA non-coding downstream 542708 61338539 ~ 61352006 (+)
XLOC_025889 NA non-coding downstream 544862 61340693 ~ 61343708 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000351_01271637_01292143 TSEN54 coding CI01000351 null 1271637 ~ 1292143 (+)