XLOC_036722 (ybx1)


Basic Information

Item Value
gene id XLOC_036722
gene name ybx1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007119.7
NCBI id CM002892.2
chromosome length 54304671
location 47143829 ~ 47152086 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00071704
TAGATTGGGGAATGGGTGGAGAGATGTGACAGAATATCGTCCGGCATTTTTACTCAGTCCGTCCAGTTCGATCGGCAACGGGAGCGGAGAAAGGAAAGCGGAGAGCCCGAAGGCAGCAGCCCCCACCACCGCCGGCCCAGGTTACCATCTAGCACCGGGAAAACACACTAGAGAGCCACCGCCGGCTTTACCAACAAGAAAACAACATGAGCAGCGAGGCCGAGACACAACAGCCGCCGCAGCCTGCCGCCGACGCGGAGAGCCCGTCCAGCCCGGCAGCCGCAGCTACCGCGGGGGATAAGAAGGTCATCGCAACAAAAGTTTTGGGGACAGTGAAATGGTTCAATGTAAGGAACGGCTACGGTTTCATCAACAGGAATGACACAAAGGAAGATGTCTTTGTGCATCAGACCGCCATTAAAAAGAACAACCCCAGGAAATATCTCCGTAGCGTTGGGGACGGAGAGACTGTGGAGTTCGACGTGGTAGAAGGGGAGAAGGGGGCTGAGGCAGCAAATGTTACCGGCCCGGGTGGCGTTCCTGTGCAGGGTAGTAAGTATGCAGCTGACAGGAACCGTTACAGGCGGTACCCACGCAGGAGGGCCCCACCTCGCGACTACCAGGAGAACTATCAGAGCGACCCTGAGGCAGAGCCCCGGGAGAAGAGAGAGGGGGCAGAGAGCGCCCCCGAGGGGGagatgcagcagcagcagcgcagACCCACTTACCCCGGCAGACGGCGCTACCCACCATACTTCGTGCGGAGGCGTTACGGCAGACGCCCCCCCTACACCAACTCACAAAGAGGAGAGATGACAGAGGGTGGTGAAGGTGAAGAGAACCAAGGGGGTCCAGACCAGGGCAACAAACCAATGAGGCAGAACTACTACAGAGGCTTCCGACCAAGGGGTCCCTCACGTCCCCGGCCAGTGCGGGACGGAGAGGAGGATAAGGAGAACCAGAGCGAGAGCGGACAGAACCAGGAGCCCCGTCAGCGCCGCTACCGTCGCAACTTCAACTACCGCCGCAGACGCCCCCAGACAACCAAGCCTCAGGACGGCAAGGACAGCAAGGCAGCCGACGCATCAGCCGACAAATCAGCCGCTCCCGAAGCCGAACAGGGCGGAGCAGATTAAACCGCCACCGGCTTAAACATCCAGACCATCCGGCCGGTTTTGTCAAGAAGAAACATCCAACATCTGAGCAATAAGAAACAGATATGACTTCGATCGTCTAAGCTTGCAAAAATGCATTTCGACCAGATTACCACCGATTGCCTGCAGACTCtatgcagacttttttttttgtttgttttgtttttccattaTTTTTGTGACAGCTAAAACTTTTGGGGAAACAGCAGATGTTTTTCTAAATCGGTCTTAAGTTTTTACACCAAAtggtttttaaatgtaatttgataTCTGGTcagtttgacatttttaaataactttttatgtATCCAAACATGAATTTTAACAAAAGGCAAGCTGAAATAAAAACCAGAAACATTAA
>TCONS_00071705
GGAGAAAGGAAAGCGGAGAGCCCGAAGGCAGCAGCCCCCACCACCGCCGGCCCAGGTTACCATCTAGCACCGGGAAAACACACTAGAGAGCCACCGCCGGCTTTACCAACAAGAAAACAACATGAGCAGCGAGGCCGAGACACAACAGCCGCCGCAGCCTGCCGCCGACGCGGAGAGCCCGTCCAGCCCGGCAGCCGCAGCTACCGCGGGGGATAAGAAGGTCATCGCAACAAAAGTTTTGGGGACAGTGAAATGGTTCAATGTAAGGAACGGCTACGGTTTCATCAACAGGAATGACACAAAGGAAGATGTCTTTGTGCATCAGACCGCCATTAAAAAGAACAACCCCAGGAAATATCTCCGTAGCGTTGGGGACGGAGAGACTGTGGAGTTCGACGTGGTAGAAGGGGAGAAGGGGGCTGAGGCAGCAAATGTTACCGGCCCGGGTGGCGTTCCTGTGCAGGGTAGTAAGTATGCAGCTGACAGGAACCGTTACAGGCGGTACCCACGCAGGAGGGCCCCACCTCGCGACTACCAGGAGAACTATCAGAGCGACCCTGAGGCAGAGCCCCGGGAGAAGAGAGAGGGGGCAGAGAGCGCCCCCGAGGGGGagatgcagcagcagcagcgcagACCCACTTACCCCGGCAGACGGCGCTACCCACCATACTTCGTGCGGAGGCGTTACGGCAGACGCCCCCCCTACACCAACTCACAAAGAGGAGAGATGACAGAGGGTGGTGAAGGTGAAGAGAACCAAGGGGGTCCAGACCAGGGCAACAAACCAATGAGGCAGAACTACTACAGAGGCTTCCGACCAAGCAGGGGTCCCTCACGTCCCCGGCCAGTGCGGGACGGAGAGGAGGATAAGGAGAACCAGAGCGAGAGCGGACAGAACCAGGAGCCCCGTCAGCGCCGCTACCGTCGCAACTTCAACTACCGCCGCAGACGCCCCCAGACAACCAAGCCTCAGGACGGCAAGGACAGCAAGGCAGCCGACGCATCAGCCGACAAATCAGCCGCTCCCGAAGCCGAACAGGGCGGAGCAGATTAAACCGCCACCGGCTTAAACATCCAGACCATCCGGCCGGTTTTGTCAAGAAGAAACATCCAACATCTGAGCAATAAGAAACAGATATGACTTCGATCGTCTAAGCTTGCAAAAATGCATTTCGACCAGATTACCACCGATTGCCTGCAGACTCtatgcagacttttttttttgtttgttttgtttttccattaTTTTTGTGACAGCTAAAACTTTTGGGGAAACAGCAGATGTTTTTCTAAATCGGTCTTAAGTTTTTACACCAAAtggtttttaaatgtaatttgataTCTGGTcagtttgacatttttaaataactttttatgtATCCAAACATGAATTTTAACAAAAGGCAAGCTGAAATAAAAACCAGAAACATT
>TCONS_00071706
GCGGAGAAAGGAAAGCGGAGAGCCCGAAGGCAGCAGCCCCCACCACCGCCGGCCCAGGTTACCATCTAGCACCGGGAAAACACACTAGAGAGCCACCGCCGGCTTTACCAACAAGAAAACAACATGAGCAGCGAGGCCGAGACACAACAGCCGCCGCAGCCTGCCGCCGACGCGGAGAGCCCGTCCAGCCCGGCAGCCGCAGCTACCGCGGGGGATAAGAAGGTCATCGCAACAAAAGTTTTGGGGACAGTGAAATGGTTCAATGTAAGGAACGGCTACGGTTTCATCAACAGGAATGACACAAAGGAAGATGTCTTTGTGCATCAGACCGCCATTAAAAAGAACAACCCCAGGAAATATCTCCGTAGCGTTGGGGACGGAGAGACTGTGGAGTTCGACGTGGTAGAAGGGGAGAAGGGGGCTGAGGCAGCAAATGTTACCGGCCCGGGTGGCGTTCCTGTGCAGGGTAGTAAGTATGCAGCTGACAGGAACCGTTACAGGCGGTACCCACGCAGGAGGGCCCCACCTCGCGACTACCAGGAGAACTATCAGAGCGACCCTGAGGCAGAGCCCCGGGAGAAGAGAGAGGGGGCAGAGAGCGCCCCCGAGGGGGagatgcagcagcagcagcgcagACCCACTTACCCCGGCAGACGGCGCTACCCACCATACTTCGTGCGGAGGCGTTACGGCAGACGCCCCCCCTACACCAACTCACAAAGAGGAGAGATGACAGAGGGTGGTGAAGGTGAAGAGAACCAAGGGGGTCCAGACCAGGGCAACAAACCAATGAGGCAGAACTACTACAGAGGCTTCCGACCAAGCAGGGGTCCCTCACGTCCCCGGCCAGTGCGGGACGGAGAGGAGGATAAGGAGAACCAGAGCGAGAGCGGACAGAACCAGGAGCCCCGTCAGCGCCGCTACCGTCGCAACTTCAACTACCGCCGCAGACGCCCCCAGACAACCAAGCCTCAGGACGGCAAGGACAGCAAGGCAGCCGACGCATCAGCCGACAAATCAGCCGCTCCCGAAGCCGAACAGGGCGGAGCAGATTAAACCGCCACCGGCTTAAACATCCAGACCATCCGGCCGGGTGGGTGACGCCGTTTCATTTCAGCTAGTACTGCATGTACTTTAACATACTTGATCTTCAAGTGTGTTGCAATTTGTACAGTAGCAttcttttgtttcgttttttctATAATTGTTTTTGTTGACAGAGTCTCATGAAAGATCTGAAAGGCACATTTtgcttaataaatgttttgttgttgccTAAAGGAAATAAAGAATATTTGAAGC
>TCONS_00071707
CAGTTCGATCGGCAACGGGAGCGGAGAAAGGAAAGCGGAGAGCCCGAAGGCAGCAGCCCCCACCACCGCCGGCCCAGGTTACCATCTAGCACCGGGAAAACACACTAGAGAGCCACCGCCGGCTTTACCAACAAGAAAACAACATGAGCAGCGAGGCCGAGACACAACAGCCGCCGCAGCCTGCCGCCGACGCGGAGAGCCCGTCCAGCCCGGCAGCCGCAGCTACCGCGGGGGATAAGAAGGTCATCGCAACAAAAGTTTTGGGGACAGTGAAATGGTTCAATGTAAGGAACGGCTACGGTTTCATCAACAGGTAAATAACTTTCAGCTTCTGAAGAGCTATCTAATATAATATGTGGGTCAGGGAACATCCACAATCCTATTAGAGCTTTGCTTACAAAGCAGGACCTGACATGCACTAGCATGCTAATATTTATCCAAATATTTAACTTGCTGCTCAACTGAACATGCTTGTTTACACTAAGTCCTCGGCTTTTAATGTTTTCACTTTCTTTATTTTTGCAGGAATGACACAAAGGAAGATGTCTTTGTGCATCAGACCGCCATTAAAAAGAACAACCCCAGGAAATATCTCCGTAGCGTTGGGGACGGAGAGACTGTGGAGTTCGACGTGGTAGAAGGGGAGAAGGGGGCTGAGGCAGCAAATGTTACCGGCCCGGGTGGCGTTCCTGTGCAGGGTAGTAAGTATGCAGCTGACAGGAACCGTTACAGGCGGTACCCACGCAGGAGGGCCCCACCTCG
>TCONS_00071708
TCGATCGGCAACGGGAGCGGAGAAAGGAAAGCGGAGAGCCCGAAGGCAGCAGCCCCCACCACCGCCGGCCCAGGTTACCATCTAGCACCGGGAAAACACACTAGAGAGCCACCGCCGGCTTTACCAACAAGAAAACAACATGAGCAGCGAGGCCGAGACACAACAGCCGCCGCAGCCTGCCGCCGACGCGGAGAGCCCGTCCAGCCCGGCAGCCGCAGCTACCGCGGGGGATAAGAAGGTCATCGCAACAAAAGTTTTGGGGACAGTGAAATGGTTCAATGTAAGGAACGGCTACGGTTTCATCAACAGGAATGACACAAAGGAAGATGTCTTTGTGCATCAGACCGCCATTAAAAAGAACAACCCCAGGAAATATCTCCGTAGCGTTGGGGACGGAGAGACTGTGGAGTTCGACGTGGTAGAAGGGGAGAAGGTGAGCTTTTAGTCGTAGCTTAGTTTGACTCAAACAAAAGTTTCACCACACAGTTAGAAATATTAGGCTTGAGGACTTGTTTAATAAAAGTCAAGGACAAATTATTTATTgagaaatgtattatttctttcttGCTTTTATGTAGTACTAGTCAAGCTTTgggctttaaattaaaatgcattaaacagCACAAAATCATAACAcagatgtcaaactcaatcctggagggccgcagctctgctcagtttagttc

Function

symbol description
ybx1 Enables C5-methylcytidine-containing RNA binding activity and eukaryotic initiation factor 4E binding activity. Involved in embryonic morphogenesis and mRNA stabilization. Acts upstream of or within several processes, including negative regulation of mRNA processing; negative regulation of translational initiation; and oocyte maturation. Located in nucleus. Is expressed in eye. Orthologous to several human genes including YBX1 (Y-box binding protein 1).

GO:

id name namespace
GO:0006397 mRNA processing biological_process
GO:1990428 miRNA transport biological_process
GO:0050658 RNA transport biological_process
GO:0048255 mRNA stabilization biological_process
GO:2000773 negative regulation of cellular senescence biological_process
GO:0051236 establishment of RNA localization biological_process
GO:0050686 negative regulation of mRNA processing biological_process
GO:0017148 negative regulation of translation biological_process
GO:0008544 epidermis development biological_process
GO:0048598 embryonic morphogenesis biological_process
GO:0010468 regulation of gene expression biological_process
GO:0051031 tRNA transport biological_process
GO:0048025 negative regulation of mRNA splicing, via spliceosome biological_process
GO:1900364 negative regulation of mRNA polyadenylation biological_process
GO:0045947 negative regulation of translational initiation biological_process
GO:0008380 RNA splicing biological_process
GO:0070062 extracellular exosome cellular_component
GO:0005576 extracellular region cellular_component
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0005515 protein binding molecular_function
GO:0008190 eukaryotic initiation factor 4E binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0035198 miRNA binding molecular_function

KEGG:

id description
ko03000 Transcription factors
ko03019 Messenger RNA biogenesis
ko03041 Spliceosome

ZFIN:

id description
ZDB-GENE-000629-3 Enables C5-methylcytidine-containing RNA binding activity and eukaryotic initiation factor 4E binding activity. Involved in embryonic morphogenesis and mRNA stabilization. Acts upstream of or within several processes, including negative regulation of mRNA processing; negative regulation of translational initiation; and oocyte maturation. Located in nucleus. Is expressed in eye. Orthologous to several human genes including YBX1 (Y-box binding protein 1).

Ensembl:

ensembl_id ENSDARG00000004757

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00071704 False 1515 mRNA 0.53 8 47143829 47152086
TCONS_00071705 False 1431 mRNA 0.54 8 47143831 47152001
TCONS_00071706 False 1302 mRNA 0.56 7 47144541 47152003
TCONS_00071707 False 762 lncRNA 0.52 4 47147364 47152023
TCONS_00071708 True 686 lncRNA 0.49 4 47148966 47152019

Neighbor

gene id symbol gene type direction distance location
XLOC_036721 NA coding downstream 49891 47090111 ~ 47093938 (-)
XLOC_036720 hes2.1 coding downstream 217570 46921333 ~ 46926259 (-)
XLOC_036719 hes2.2 coding downstream 246095 46896445 ~ 46897734 (-)
XLOC_036718 acot7 coding downstream 249467 46758264 ~ 46894362 (-)
XLOC_036717 gpr153 coding downstream 443551 46656170 ~ 46700278 (-)
XLOC_036723 ppih coding upstream 618 47152704 ~ 47206399 (-)
XLOC_036724 NA coding upstream 46548 47198634 ~ 47199165 (-)
XLOC_036725 pimr189 coding upstream 57573 47209659 ~ 47212686 (-)
XLOC_036726 NA coding upstream 104892 47256978 ~ 47258976 (-)
XLOC_036727 CR792439.2 coding upstream 123210 47275296 ~ 47275410 (-)
XLOC_036716 NA non-coding downstream 514451 46627663 ~ 46629378 (-)
XLOC_036701 NA non-coding downstream 1671612 45468994 ~ 45472217 (-)
XLOC_036699 CU695141.1 non-coding downstream 1732084 45411581 ~ 45411745 (-)
XLOC_036696 NA non-coding downstream 1940859 45200851 ~ 45202970 (-)
XLOC_036728 NA non-coding upstream 150285 47302371 ~ 47315226 (-)
XLOC_036730 LO017720.1 non-coding upstream 353799 47505885 ~ 47506001 (-)

Expression


Co-expression Network