smx5 (lsm2,LSM2,smx5)


Basic Information

Item Value
gene id smx5
gene name lsm2,LSM2,smx5
gene type misc
species striped catfish (Pangasianodon hypophthalmus)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_047596.1
NCBI id CM018542.1
chromosome length 35203048
location 19534345 ~ 19537197 (+)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome

Sequence

>TU35395
GATGACGTAACTTGCTCACAAAATAGCGCGTGAAAATgCTTTTCTACTCATTCTTCAAGTCCTTGGTGGGTAAAGACGTGGTGGTGGAGTTAAAAAATGACTTGAGCATATGTGGGACCCTACACTCAGTGGATCAGTATCTGAACATCAAACTCACAGATATCAGTGTCACTGACCCTGAAAAGTATCCTCACATGTTGTCCGTGAAGAACTGCTTCATCCGGGGGTCTGTGGTGCGGTACGTTCAGCTCCCGGCTGATGAGGTGGACACACAGCTACTCCAGGATGCAGCACGCAAAGAAGCCATGCAGCAGAAACAATGATTCACCTGGTTTTGTTCTTTTGCTTTGTGGTGGACTTGTACAAAATATAACTGCATTGGTTTACCTTTTTCTTTTAAGCTCAGATTTTGTATAGTGTTGATAATGTAAGGAATGCTGTATGTTTTTCAGTACATGTTGACGAGATACGAGTGGCAGATTCTTAGAAAATGAGGTTTCTCTCTTCACACTTCAGgcttaattaatgttttttgaaATACAAATGGGGTTGCCTGGGGTTTGACTTTATCAGATTAAGTTGTAGCACTCAGCCCTTAAATTCAGAATCGCCCTGACCTAGG
>XM_034310151.1
GACGAGTCCAATGTTAACCAATGGATAGGAAGAATAATACAGCCCTCTAGTTGCTGACCAATGGGAAGGTGGATTGATTGTCATCTGTCCGTATTTGATGACGTAACTTGCTCACAAAATAGCGCGTGAAAATgCTTTTCTACTCATTCTTCAAGTCCTTGGTGGGTAAAGACGTGGTGGTGGAGTTAAAAAATGACTTGAGCATATGTGGGACCCTACACTCAGTGGATCAGTATCTGAACATCAAACTCACAGATATCAGTGTCACTGACCCTGAAAAGTATCCTCACATGTTGTCCGTGAAGAACTGCTTCATCCGGGGGTCTGTGGTGCGGTACGTTCAGCTCCCGGCTGATGAGGTGGACACACAGCTACTCCAGGATGCAGCACGCAAAGAAGCCATGCAGCAGAAACAATGATTCACCTGGTTTTGTTCTTTTGCTTTGTGGTGGACTTGTACAAAATATAACTGCATTGGTTTACCTTTTTCTTTTAAGCTCAGATTTTGTATAGTGTTGATAATGTAAGGAATGCTGTATGTTTTTCAGTACATGTTGACGAGATACGAGTGGCAGATTCTTAGAAAATGAGGTTTCTCTCTTCACACTTCAGgcttaattaatgttttttgaaATACAAATGGGGTTGCCTGGGGTTTGACTTTATCAGATTAAGTTGTAGCACTCAGCCCTTAAATTCAGAATCGCCCTGACCTAGGTATagatgtttatatgtttaaatacattttattacatttagctgttttttttttgtttttttgtttttttactgaatcAGAAAGCAAGAAGAACCCCaaaataattaatcatattCAGACACAGTAAAGTGGCCTGCCTAGGTTttgttgaaatgaaaataaaactgatacTGTGTTGAATAA

Function

symbol description
smx5 Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of Lsm1-7-Pat1 complex and nucleus. Predicted to be active in P-body. Orthologous to human LSM2 (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated).
lsm2 Enables small GTPase binding activity. Involved in mRNA splicing, via spliceosome. Acts upstream of or within mRNA catabolic process and spliceosomal tri-snRNP complex assembly. Located in cytoplasm and nucleoplasm. Part of Lsm2-8 complex; U4/U6 x U5 tri-snRNP complex; and spliceosomal complex.

NR:

description
U6 snRNA-associated Sm-like protein LSm2

GO:

id name namespace
GO:0043928 exonucleolytic catabolism of deadenylated mRNA biological_process
GO:0000244 spliceosomal tri-snRNP complex assembly biological_process
GO:0071013 catalytic step 2 spliceosome cellular_component
GO:0046540 U4/U6 x U5 tri-snRNP complex cellular_component
GO:0005829 cytosol cellular_component
GO:0005654 nucleoplasm cellular_component
GO:0017070 U6 snRNA binding molecular_function
GO:0019901 protein kinase binding molecular_function

KEGG:

id description
K12621 LSM2; U6 snRNA-associated Sm-like protein LSm2

RNA

RNA id representative length rna type GC content exon number start site end site
TU35395 False 622 TUCP 0.42 5 19534441 19537014
XM_034310151.1 True 901 mRNA 0.39 5 19534345 19537197

Neighbor

gene id symbol gene type direction distance location
inpp5d inpp5d coding upstream 1540 19509832 ~ 19532805 (+)
gpr17 gpr17,LOC107717943,LOC107752663,LOC107694121,LOC107590682 coding upstream 27488 19501596 ~ 19506857 (+)
LOC113527823 LOC108271983,LOC108427680,LOC108271985 coding upstream 33738 19477978 ~ 19500607 (+)
LOC117595738 LOC108271985,LOC108271983,LOC108427680 coding upstream 59612 19465393 ~ 19474733 (+)
sap130a sap130a,LOC108271984,LOC107696772,LOC107590658,LOC107552246,LOC108427679 coding upstream 71028 19448315 ~ 19463317 (+)
lpp lpp,LOC108271779,LOC108427685,LOC107717931,LOC107590653,LOC107684332,LOC107696776,LOC107752632 coding downstream 51630 19588827 ~ 19803848 (+)
tprg1 LOC108272012 coding downstream 317933 19855130 ~ 19883588 (+)
tp63 tp63,LOC107574491,LOC103365775 coding downstream 347564 19884761 ~ 19956034 (+)
rpl5b LOC103397662,LOC103368809,LOC104921761,LOC101078338,LOC107590646 coding downstream 567007 20104204 ~ 20112519 (+)
LOC113537321 NA coding downstream 572933 20110130 ~ 20110225 (+)
G29819 NA non-coding upstream 117437 19415605 ~ 19416908 (+)
G29792 NA non-coding upstream 275079 19259048 ~ 19259266 (+)
G29674 NA non-coding upstream 332246 19200315 ~ 19202099 (+)
G29656 NA non-coding upstream 338936 19192549 ~ 19195409 (+)
G29641 NA non-coding upstream 483302 19050824 ~ 19051043 (+)
LOC113533855 NA non-coding downstream 788 19537985 ~ 19540117 (+)
G29984 NA non-coding downstream 3432 19540629 ~ 19540910 (+)
G29985 NA non-coding downstream 3742 19540939 ~ 19541248 (+)
LOC117596099 NA non-coding downstream 15855 19553052 ~ 19582043 (+)
G29999 NA non-coding downstream 28613 19565810 ~ 19566023 (+)
LOC113533886 espnl other upstream 447134 19061097 ~ 19087211 (+)
boka bok,LOC107733256,LOC107752647,LOC107694130,LOC107696759 other upstream 585608 18932683 ~ 18948737 (+)
G29569 hdlbpa,hdlbp,LOC107694132,LOC107733253 other upstream 698624 18774770 ~ 18835721 (+)
trnai-aau NA other upstream 716870 18817402 ~ 18817475 (+)
tomm6 tomm6 other upstream 3133234 16398245 ~ 16401111 (+)
LOC113543059 c11h1orf146 other downstream 462849 20000046 ~ 20020226 (+)
dlg1 dlg1,LOC108271975,LOC108427717,LOC107738730 other downstream 999776 20536973 ~ 20658080 (+)
insl5a insl5 other downstream 1477641 21014838 ~ 21017867 (+)
tmem69 tmem69 other downstream 3060398 22597595 ~ 22603436 (+)
uhmk1 uhmk1,LOC107692420 other downstream 4096409 23633606 ~ 23653555 (+)

Expression


Co-expression Network