XLOC_003896 (lsm4)


Basic Information

Item Value
gene id XLOC_003896
gene name lsm4
gene type coding
species zebrafish (Danio rerio)
category of species model fish

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

Sequence

>TCONS_00007457
GGGACTTTTGCTTTGACAACTTCCGCTTTCACCTGGAAGTACAACAGTAAGTGGTTTGCAGATCGCCTTGTGCTGCGAAGAAGATTCACAGAAAATCATTTGTGATTGAAGTCTTCAGTGGATTAAAACTTCATATAAAGACTGATTGGTCATTCAGCTGACATGCTCCCGTTATCTTTACTGAAGACGGCACAGAACCACCCGATGCTGGTGGAGTTAAAGAATGGCGAGACATACAACGGCCATCTGGTCAGCTGCGACAACTGGATGAATATAAACTTGAGAGAAGTTATTTGCACTTCACGGGATGGAGATAAGTTTTGGAGGATGCCAGAATGCTACATAAGAGGAAGCACCATTAAATACTTGCGAATCCCTGATGAAATTATAGATATGGTGAAAGAGGAAGTGGTGTCAAAGGGCCGTGGCCGGGGTGGCATGCAGCAGAATAAGCCACAAGGAAAGGGCAGAGGAGGTGGACCTGGAAGAGGCGGCGGACCTGGCAGAGGTGTTTTTGGTGGCCGTGGCAGAGGCATGCAGGGATCTGGCCGTGGACAGCAACAAGACAAAAAGCCTGGAAAACAACAAGTTTGATCATCGACCAGAAAGAACGAGTTTAATTTGAAATGGACGTCCTGGATCTCCGTGAAGATTTTAATTTGGTGATGTTGATTTAAAGATGCTCTTTCATTCGttctaaactgttttattttgtcttcAGTCATTCGGTGCATGTTTTCACATTTCTCTTTTTGTGCTTTAAAACACAACCATGCTGTAAGTTTGACTTGTCTATATGCACTTGTGAATAAACGATTTTTGTTAAATATGG
>TCONS_00007458
gatgatgtgtggatgatttACACGgggcataactaagcaacacagcGATCTGTTAAGGAGGAAGTACTCCCGTTATCTTTACTGAAGACGGCACAGAACCACCCGATGCTGGTGGAGTTAAAGAATGGCGAGACATACAACGGCCATCTGGTCAGCTGCGACAACTGGATGAATATAAACTTGAGAGAAGTTATTTGCACTTCACGGGATGGAGATAAGTTTTGGAGGATGCCAGAATGCTACATAAGAGGAAGCACCATTAAATACTTGCGAATCCCTGATGAAATTATAGATATGGTGAAAGAGGAAGTGGTGTCAAAGGGCCGTGGCCGGGGTGGCATGCAGCAGAATAAGCCACAAGGAAAGGGCAGAGGAGGTGGACCTGGAAGAGGCGGCGGACCTGGCAGAGGTGTTTTTGGTGGCCGTGGCAGAGGCATGCAGGGATCTGGCCGTGGACAGCAACAAGACAAAAAGCCTGGAAAACAACAAGTTTGATCATCGACCAGAAAGAACGAGTTTAATTTGAAATGGACGTCCTGGATCTCCGTGAAGATTTTAATTTGGTGATGTTGATTTAAAGATGCTCTTTCATTCGttctaaactgttttattttgtcttcAGTCATTCGGTGCATGTTTTCACATTTCTCTTTTTGTGCTTTAAAACACAACCATGCTGTAAGTTTGACTTGTCTATATGCACTTGTGAATAAACGATTTTTGTTAAATATGG

Function

symbol description
lsm4 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).

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 ENSDARG00000023852

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00007457 False 832 mRNA 0.43 6 6859876 6868287
TCONS_00007458 True 733 mRNA 0.44 6 6859876 6868474
Loading

Neighbor

gene id symbol gene type direction distance location
XLOC_003895 NA coding downstream 59938 6792546 ~ 6799938 (-)
XLOC_003894 BX936438.1 coding downstream 77800 6780708 ~ 6782076 (-)
XLOC_003893 NA coding downstream 403576 6455034 ~ 6456300 (-)
XLOC_003892 larp6b coding downstream 407384 6446235 ~ 6452492 (-)
XLOC_003891 NA coding downstream 428528 6429973 ~ 6431348 (-)
XLOC_003897 ddx49 coding upstream 838 6869312 ~ 6880725 (-)
XLOC_003898 comp coding upstream 72915 6941389 ~ 6974022 (-)
XLOC_003899 si:ch211-253b8.2 coding upstream 108794 6977268 ~ 6985463 (-)
XLOC_003900 zgc:173548 coding upstream 118115 6986589 ~ 6989598 (-)
XLOC_003901 cdh27 coding upstream 133474 7001948 ~ 7030047 (-)
XLOC_003938 BX324177.10 misc upstream 4470330 11338804 ~ 11339100 (-)
XLOC_003942 BX324177.17 misc upstream 4499120 11367594 ~ 11367890 (-)
XLOC_003943 BX324177.3 misc upstream 4501981 11370455 ~ 11370653 (-)
XLOC_003944 BX324177.4 misc upstream 4512430 11380904 ~ 11381204 (-)
XLOC_003945 BX324177.6 misc upstream 4515359 11383833 ~ 11384130 (-)
XLOC_003887 NA non-coding downstream 535319 6316654 ~ 6324557 (-)
XLOC_003904 CR925817.2 non-coding upstream 247773 7116247 ~ 7116363 (-)
XLOC_003908 NA non-coding upstream 477326 7345800 ~ 7349497 (-)
XLOC_003912 NA non-coding upstream 905358 7773832 ~ 7796332 (-)
XLOC_003920 CR847563.2 non-coding upstream 1608487 8476961 ~ 8515750 (-)
XLOC_003922 NA non-coding upstream 2115177 8983651 ~ 9523184 (-)

Expression

Expression of XLOC_003896(lsm4) in the Zebrafish Sample from each Developmental Stage of PRJEB12982

Boxplot with 18 boxes. Box plot charts are typically used to display groups of statistical data. Each data point in the chart can have up to 5 values: minimum, lower quartile, median, upper quartile, and maximum.
The chart has 1 X axis displaying categories.
The chart has 1 Y axis displaying Expression. Range: 0 to 400.
End of interactive chart.

Expression of XLOC_003896(lsm4) in the Zebrafish Sample of PRJEB12982

Bar chart with 360 bars.
The chart has 1 X axis displaying categories.
The chart has 1 Y axis displaying Expression. Range: 0 to 400.
End of interactive chart.

Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) G245467 NA non-coding CI01000057 null 4455149 ~ 4457859 (+)
tiger barb (Puntius tetrazona) tomm7 NA misc NW_025048355.1 JAEQBD010000700.1 1536021 ~ 1541873 (+)