XLOC_009648 (LIN28A)


Basic Information

Item Value
gene id XLOC_009648
gene name LIN28A
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 4654333 ~ 4686245 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00019345
TGTTGGTCATCCTGGAGAGTAAGTGATTGGGAATCACGTGGACTTGACCGAAACAGGCAGAGAGGGGGTCGGCCAGCGAGAAGCATCAGTACAGGGTCACCAAACCACCGAGAGACCACCTGGAGGTCCGAGTTTTAACGCAAACATCCAGAACTGAACCCCGGGAGTTAAGCATAGAGGAGGCCAGAATTGAGGAAACCCATGGCAGAGGGAGGCTGTGCGAAgacagaggaggaggaggggcaGGCCGCAGAGGAAGACCCTCGGCCGTATCATGGTGTGGGTGTGTGCAAGTGGTTCAATGTTCGGATGGGTTTTGGATTCCTATCCATGAACACACGGGACGGTGTGCCTTTGGAAACTCCAGTTGATGTATTTGTCCATCAGAGTAAACTGCACATGGAGGGTTTCCGCAGTCTGAAGGAGGGTGAGTCTGTAGAGTTCACCTTCAAGAAGTCATCCAAAGGCCTGGAGTCTGTGCGGGTGACGGGGCCCGGAGGAGCTCACTGTGTGGGCAGCGACCGGAGACCCAAAGGCAAGAGTGTCCAGAAACGCCGGGCTAAAGGAGACAGGTGCTACAACTGTGGCGGTCTGGACCACCACGCCAAGGAGTGCAAACTTCCTCCCCAACCCAAAAGATGCCATTTCTGCCAAAGTGTCGCACATATGGTGGCAAACTGCCCCGTCAAAGCCCAGCAGTCGACACAAGGCTCTCAGGGAAAGTCTGCGGGTCAGAAACAAGAGGAAGCGGATCAAAATCATTCACCACCAGCCACCGACTGA
>TCONS_00019346
GCAGGAGGCTGTGCGAAgacagaggaggaggaggggcaGGCCGCAGAGGAAGACCCTCGGCCGTATCATGGTGTGGGTGTGTGCAAGTGGTTCAATGTTCGGATGGGTTTTGGATTCCTATCCATGAACACACGGGACGGTGTGCCTTTGGAAACTCCAGTTGATGTATTTGTCCATCAGAGTAAACTGCACATGGAGGGTTTCCGCAGTCTGAAGGAGGGTGAGTCTGTAGAGTTCACCTTCAAGAAGTCATCCAAAGGCCTGGAGTCTGTGCGGGTGACGGGGCCCGGAGGAGCTCACTGTGTGGGCAGCGACCGGAGACCCAAAGGCAAGAGTGTCCAGAAACGCCGGGCTAAAGGAGACAGGTGCTACAACTGTGGCGGTCTGGACCACCACGCCAAGGAGTGCAAACTTCCTCCCCAACCCAAAAGATGCCATTTCTGCCAAAGTGTCGCACATATGGTGGCAAACTGCCCCGTCAAAGCCCAGCAGTCGACACAAGGCTCTCAGGGAAAGTCTGCGGGTCAGAAACAAGAGGAAGCGGATCAAAATCATTCACCACCAGCCACCGACTGACACCACGCTTGAAAACCAATCACACACCACTGCACTGgataaacacacatgcataatGCTGCTGCTGGAACTTCCTCAGGTCTAAATAAGCAAGGAGAACATGACTTTCATATCCTTTTTTAATGGTTTGAAGGTGTGTTCACATCAAGAATGATGAATATACCCTCTCAGAAACATCTGCTTATTAAAAGTTGCCGTATTTATGTGTTTTCCACTTATttgtggttgtgaattgcattatgggatgttgatctctgctctgtccacttttgatgtagAAAATTCACTTCTACAGTTGAACAAAGAGACTTTTAG

Function

symbol description
lin28a Enables RNA binding activity and polysome binding activity. Involved in RNA metabolic process; positive regulation of cytoplasmic translation; and stem cell population maintenance. Located in cytoplasmic ribonucleoprotein granule; cytosol; and nucleolus. Part of polysome.

GO:

id name namespace
GO:0010629 negative regulation of gene expression biological_process
GO:0043009 chordate embryonic development biological_process
GO:0019827 stem cell population maintenance biological_process
GO:2000767 positive regulation of cytoplasmic translation biological_process
GO:0031047 gene silencing by RNA biological_process
GO:0031054 pre-miRNA processing biological_process
GO:0031099 regeneration biological_process
GO:0031123 RNA 3'-end processing biological_process
GO:0010587 miRNA catabolic process biological_process
GO:0005783 endoplasmic reticulum cellular_component
GO:0005791 rough endoplasmic reticulum cellular_component
GO:0000932 P-body cellular_component
GO:0005844 polysome cellular_component
GO:0005634 nucleus cellular_component
GO:0010494 cytoplasmic stress granule cellular_component
GO:0005730 nucleolus cellular_component
GO:0005737 cytoplasm cellular_component
GO:1905538 polysome binding molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040426-747 Predicted to enable RNA binding activity and polysome binding activity. Acts upstream of or within chordate embryonic development; negative regulation of gene expression; and regeneration. Predicted to be located in P-body; cytoplasmic stress granule; and nucleus. Predicted to be part of polysome. Is expressed in several structures, including Kupffer's vesicle; central nervous system; digestive system; neural plate; and neural tube. Orthologous to human LIN28A (lin-28 homolog A).

Ensembl:

ensembl_id ENSDARG00000004328

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00019345 False 783 mRNA 0.55 4 4654333 4685930
TCONS_00019346 True 891 mRNA 0.49 3 4658250 4686245

Neighbor

gene id symbol gene type direction distance location
XLOC_009647 NA coding upstream 94421 4559111 ~ 4559912 (+)
XLOC_009646 tfpt coding upstream 113419 4531730 ~ 4540914 (+)
XLOC_009645 ttc29 coding upstream 141538 4497302 ~ 4512795 (+)
XLOC_009644 NA coding upstream 227039 4422621 ~ 4427294 (+)
XLOC_009643 NA coding upstream 318469 4330959 ~ 4335864 (+)
XLOC_009649 mecr coding downstream 8830 4695075 ~ 4707668 (+)
XLOC_009650 NA coding downstream 22490 4708735 ~ 4711728 (+)
XLOC_009651 themis2 coding downstream 39584 4725829 ~ 4746492 (+)
XLOC_009652 ube3d coding downstream 84021 4770266 ~ 4796565 (+)
XLOC_009653 ibtk coding downstream 152563 4838808 ~ 4895521 (+)
XLOC_009642 NA non-coding upstream 337726 4316169 ~ 4316607 (+)
XLOC_009640 NA non-coding upstream 479309 4132537 ~ 4175024 (+)
XLOC_009654 FO722028.1 non-coding downstream 188119 4874364 ~ 4874481 (+)
XLOC_009659 NA non-coding downstream 813029 5499274 ~ 5502699 (+)
XLOC_009668 NA non-coding downstream 1709058 6395303 ~ 6421449 (+)
XLOC_009675 NA non-coding downstream 2431902 7118147 ~ 7118568 (+)

Expression


Co-expression Network