XLOC_000426 (lsm6)


Basic Information

Item Value
gene id XLOC_000426
gene name lsm6
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 36194761 ~ 36204000 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00000729
CGAGCTCATTGGTCAGCAGTCGCTCAGTCGAAACGTGCGGTTAACGTTGCTAAACGACATAGctaaaATGAGTCTCCGAAAGCAGACACCAAGTGATTTCCTGAAGCAGATCATTGGGAGGCCAGTGGTGGTGAAACTGAACTCTGGTGTCGATTACAGAGGAGTCCTGGCCTGCCTTGACGGCTACATGAATATTGCGGTGGAACAGACAGAGGAATATGTCAACGGCCAACTGAAGAACAAGTATGGAGATGCATTTCTCAGAGGAAACAATGTGTTATACATCAGCACCCAGAAGAGGAAGATGTGAAGCTGCTTTACTTATTTCTTCATGCGTTGTTAGAGAAGTCAATTGTTTACTGTTAATATTCATAAATCCTTTGTTAGCTGATGATGATGTCTAAgtttgttaaatgttttgtaaCACACATTTGCTGTCCTGCAGAACGAAGCAGTAGCATTTGTTTTCCAACAATAAATTGTGTTCATGTTTCCCTGA
>TCONS_00000730
CGCTCAGTCGAAACGTGCGGTTAACGTTGCTAAACGACATAGGTAAATAACGTTAAATGTTGTATGCTTTAATATAAGAATGCATTCGACGTTAGTGGGGTTTTAAAAAACTGCAGCACTGTAGTTACCTTGCTAGATATACGATGACACGTTTATTAAGTGATACGTTGGGTTGGAATGCTAGCATGCTAAATTAGCCGCTTATCGATAACGTTCACCGGCAATTTCCAAACAAATAAGGTTAAACCTCTTCTGGAAACCCCTTATGTGGTTTAAAATAAACGTCTTTActaaaATGAGTCTCCGAAAGCAGACACCAAGTGATTTCCTGAAGCAGATCATTGGGAGGCCAGTGGTGGTGAAACTGAACTCTGGTGTCGATTACAGAGGAGTCCTGGCCTGCCTTGACGGCTACATGAATATTGCGGTGGAACAGACAGAGGAATATGTCAACGGCCAACTGAAGAACAAGTATGGAGATGCATTTCTCAGAGGAAACAATGTGTTATACATCAGCACCCAGAAGAGGAAGATGTGAAGCTGCTTTACTTATTTCTTCATGCGTTGTTAGAGAAGTCAATTGTTTACTGTTAATATTCATAAATCCTTTGTTAGCTGATGATGATGTCTAAgtttgttaaatgttttgtaaCACACATTTGCTGTCCTGCAGAACGAAGCAGTAGCATTTGTTTTCCAACAATAAATTGTGTTCATGTTTCCCTG

Function

symbol description
lsm6 Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome and maturation of SSU-rRNA. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U4/U6 x U5 tri-snRNP complex; U6 snRNP; and sno(s)RNA-containing ribonucleoprotein complex. Predicted to be active in P-body and nucleolus. Orthologous to human LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated).

GO:

id name namespace
GO:0006397 mRNA processing biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0030490 maturation of SSU-rRNA biological_process
GO:0008380 RNA splicing biological_process
GO:0046540 U4/U6 x U5 tri-snRNP complex cellular_component
GO:0000932 P-body cellular_component
GO:0005634 nucleus cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005688 U6 snRNP cellular_component
GO:0005730 nucleolus cellular_component
GO:0005732 small nucleolar ribonucleoprotein complex cellular_component
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-040625-50 Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome and maturation of SSU-rRNA. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U4/U6 x U5 tri-snRNP complex; U6 snRNP; and sno(s)RNA-containing ribonucleoprotein complex. Predicted to be active in P-body and nucleolus. Orthologous to human LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated).

Ensembl:

ensembl_id ENSDARG00000036995

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00000729 False 499 mRNA 0.42 4 36194761 36204000
TCONS_00000730 True 726 mRNA 0.40 4 36194781 36203999

Neighbor

gene id symbol gene type direction distance location
XLOC_000425 BX324156.1 coding upstream 40384 36154261 ~ 36154377 (+)
XLOC_000424 zgc:152968 coding upstream 191987 35985813 ~ 36002774 (+)
XLOC_000423 mmaa coding upstream 224502 35956435 ~ 35970259 (+)
XLOC_000422 BX276105.1 coding upstream 240448 35949269 ~ 35954313 (+)
XLOC_000421 NA coding upstream 296324 35896392 ~ 35898437 (+)
XLOC_000427 pou4f2 coding downstream 232936 36436936 ~ 36440301 (+)
XLOC_000428 ednraa coding downstream 408660 36612660 ~ 36702355 (+)
XLOC_000429 tmem184c coding downstream 518122 36722122 ~ 36746569 (+)
XLOC_000430 arhgap10 coding downstream 567954 36771954 ~ 36913091 (+)
XLOC_000431 NA coding downstream 762000 36966000 ~ 36966282 (+)
XLOC_000415 NA non-coding upstream 1101249 35034294 ~ 35093512 (+)
XLOC_000414 NA non-coding upstream 1333704 34857368 ~ 34861057 (+)
XLOC_000408 NA non-coding upstream 1740314 34450659 ~ 34454447 (+)
XLOC_000432 FO704615.1 non-coding downstream 919642 37123642 ~ 37123772 (+)
XLOC_000436 NA non-coding downstream 1387258 37591258 ~ 37638367 (+)
XLOC_000439 NA non-coding downstream 1629347 37833347 ~ 37834392 (+)
XLOC_000440 CT583668.1 non-coding downstream 1792459 37996459 ~ 37996577 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
rainbow trout (Oncorhynchus mykiss) LOC110534533 lsm6 misc NC_048574.1 CM023228.2 67947494 ~ 67949358 (-)
tiger barb (Puntius tetrazona) G32956 NA non-coding NC_056703.1 CM032072.1 3388301 ~ 3389487 (+)