XLOC_016969


Basic Information

Item Value
gene id XLOC_016969
gene name NA
gene type non-coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007113.7
NCBI id CM002886.2
chromosome length 59640629
location 56642138 ~ 56655769 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00033426
GTGGTCTTGTGCCGCAGTGCTACTAGTATGTGGTTGTTTCAGAGAGCGCTGTTGGTCGGAGCGGTGGGCAGCAAGAGCTTCGCCAGAGCAATGGGGTTATGTGTGTATCATCACAAACGTAGCCTCTAAATGAGGTAAAACTCCAGTAAACTACACTCAGCTTGCGGCAATGCACGTCACGTACGCTGAGAAGGGTTTACGCATCCTGGGCTTCCCCTGCAACCAGTTCGGAAAGCAGGAGCCTGGAAGTGAAGCGGAGATTAAGGAGTTTGCTAAAGGCTACAATGCAGAGTTTGATCTGTTCAGTAAGATCGATGTGAACGGAGACGCAGCTCATCCTCTCTGGAAGTGGATGAAGGAGCAGCCCAAAGGCAGAGGAACACTGGGGAACAACATCAAGTGGAATTTCACCAAGTTCCTCATTGATAGAGAGGGTCAGGTTGTGAAGAGGTACGGACCAATGGACGATCCAAGCGTGGTGGAGAAGGATCTTCCCAAGTACCTGTAGAGTGTGTATGCTGCGGCGTCTCCGTCCTGTGTTTTGGGCTCTGTTCTCTCTGGAGCAGAAACGCTGGACGTCTGCAGGTGAAGCCCAGACGTGTGACGGCTGATCCTCAAGCCTGTGTTCAGGTGGGTTCGGCCTGATGTTCCCGACGTGCAAAAATACTGGGAAAACCCTGCAAATGTTCAGACAAGTGTGTCCAGAGAGGAGCTTCATGCACTGAAAATACACTGAGCAATCTTTTATAATCAACAGCCATAATTAAAGAGTCATGTCATCATC
>TCONS_00033130
GTGGTCTTGTGCCGCAGTGCTACTAGTATGTGGTTGTTTCAGAGAGCGCTGTTGGTCGGAGCGGTGGGCAGCAAGAGCTTCGCCAGAGCAATGtgtgcccAAGCCAATGACTGGCAGTCGGCCAAATCCATATACGAGTTCTCAGCCATAGACATTGATGGAAATGATGTTTCTCTGGAGAAATACAGGGGTTATGTGTGTATCATCACAAACGTAGCCTCTAAATGAGGTAAAACTCCAGTAAACTACACTCAGCTTGCGGCAATGCACGTCACGTACGCTGAGAAGGGTTTACGCATCCTGGGCTTCCCCTGCAACCAGTTCGGAAAGCAGGAGCCTGGAAGTGAAGCGGAGATTAAGGAGTTTGCTAAAGGCTACAATGCAGAGTTTGATCTGTTCAGTAAGATCGATGTGAACGGAGACGCAGCTCATCCTCTCTGGAAGTGGATGAAGGAGCAGCCCAAAGGCAGAGGAACACTGGGGAACAACATCAAGTGGAATTTCACCAAGTTCCTCATTGATAGAGAGGGTCAGGTTGTGAAGAGGTACGGACCAATGGACGATCCAAGCGTGGTGGAGAAGGATCTTCCCAAGTACCTGTAGAGTGTGTATGCTGCGGCGTCTCCGTCCTGTGTTTTGGGCTCTGTTCTCTCTGGAGCAGAAACGCTGGACGTCTGCAGGTGAAGCCCAGACGTGTGACGGCTGATCCTCAAGCCTGTGTTCAGGTGGGTTCGGCCTGATGTTCCCGACGTGCAAAAATACTGGGAAAACCCTGCAAATGTTCAGACAAGTGTGTCCAGAGAGGAGCTTCATGCACTGAAAATACACTGAGCAATCTTTTATAATCAACAGCCATAATTAAAGAGTCATGTCATCATC
>TCONS_00033131
cagtgtgcccAAGCCAATGACTGGCAGTCGGCCAAATCCATATACGAGTTCTCAGCCATAGACATTGATGGAAATGATGTTTCTCTGGAGAAATACAGGGGTTATGTGTGTATCATCACAAACGTAGCCTCTAAATGAGGTAAAACTCCAGTAAACTACACTCAGCTTGCGGCAATGCACGTCACGTACGCTGAGAAGGGTTTACGCATCCTGGGCTTCCCCTGCAACCAGTTCGGAAAGCAGGAGCCTGGAAGTGAAGCGGAGATTAAGGAGTTTGCTAAAGGCTACAATGCAGAGTTTGATCTGTTCAGTAAGATCGATGTGAACGGAGACGCAGCTCATCCTCTCTGGAAGTGGATGAAGGAGCAGCCCAAAGGCAGAGGAACACTGGGGAACAACATCAAGTGGAATTTCACCAAGTTCCTCATTGATAGAGAGGGTCAGGTTGTGAAGAGGTACGGACCAATGGACGATCCAAGCGTGGTGGAGAAGGATCTTCCCAAGTACCTGTAGAGTGTGTATGCTGCGGCGTCTCCGTCCTGTGTTTTGGGCTCTGTTCTCTCTGGAGCAGAAACGCTGGACGTCTGCAGGTGAAGCCCAGACGTGTGACGGCTGATCCTCAAGCCTGTGTTCAGGTGGGTTCGGCC

Function

GO:

id name namespace
GO:0030097 hemopoiesis biological_process
GO:0044085 cellular component biogenesis biological_process
GO:0030099 myeloid cell differentiation biological_process
GO:0016072 rRNA metabolic process biological_process
GO:0002520 immune system development biological_process
GO:0002262 myeloid cell homeostasis biological_process
GO:0000028 ribosomal small subunit assembly biological_process
GO:0071826 ribonucleoprotein complex subunit organization biological_process
GO:0022613 ribonucleoprotein complex biogenesis biological_process
GO:0022618 ribonucleoprotein complex assembly biological_process
GO:0043009 chordate embryonic development biological_process
GO:0006364 rRNA processing biological_process
GO:0051726 regulation of cell cycle biological_process
GO:0019538 protein metabolic process biological_process
GO:0043603 cellular amide metabolic process biological_process
GO:0043604 amide biosynthetic process biological_process
GO:1901564 organonitrogen compound metabolic process biological_process
GO:1901566 organonitrogen compound biosynthetic process biological_process
GO:0009058 biosynthetic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:0043043 peptide biosynthetic process biological_process
GO:0048534 hematopoietic or lymphoid organ development biological_process
GO:1901576 organic substance biosynthetic process biological_process
GO:0006412 translation biological_process
GO:0030218 erythrocyte differentiation biological_process
GO:0010467 gene expression biological_process
GO:0048872 homeostasis of number of cells biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0042254 ribosome biogenesis biological_process
GO:0042255 ribosome assembly biological_process
GO:0044260 cellular macromolecule metabolic process biological_process
GO:0044267 cellular protein metabolic process biological_process
GO:0000470 maturation of LSU-rRNA biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0042273 ribosomal large subunit biogenesis biological_process
GO:0042274 ribosomal small subunit biogenesis biological_process
GO:0006518 peptide metabolic process biological_process
GO:0043170 macromolecule metabolic process biological_process
GO:0034101 erythrocyte homeostasis biological_process
GO:0002181 cytoplasmic translation biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0009790 embryo development biological_process
GO:0009792 embryo development ending in birth or egg hatching biological_process
GO:0044391 ribosomal subunit cellular_component
GO:0044422 obsolete organelle part cellular_component
GO:1990904 ribonucleoprotein complex cellular_component
GO:0022625 cytosolic large ribosomal subunit cellular_component
GO:0022626 cytosolic ribosome cellular_component
GO:0022627 cytosolic small ribosomal subunit cellular_component
GO:0044444 obsolete cytoplasmic part cellular_component
GO:0044445 obsolete cytosolic part cellular_component
GO:0044446 obsolete intracellular organelle part cellular_component
GO:0005829 cytosol cellular_component
GO:0005840 ribosome cellular_component
GO:0032991 protein-containing complex cellular_component
GO:0015934 large ribosomal subunit cellular_component
GO:0015935 small ribosomal subunit cellular_component
GO:0043226 organelle cellular_component
GO:0043228 non-membrane-bounded organelle cellular_component
GO:0043229 intracellular organelle cellular_component
GO:0043232 intracellular non-membrane-bounded organelle cellular_component
GO:0005737 cytoplasm cellular_component
GO:0019843 rRNA binding molecular_function
GO:0005198 structural molecule activity molecular_function
GO:0003723 RNA binding molecular_function
GO:0003735 structural constituent of ribosome molecular_function

KEGG:

id description
ko00230 Purine metabolism
ko00240 Pyrimidine metabolism
ko03020 RNA polymerase
ko03230 Viral genome structure
ko05164 Influenza A
ko05169 Epstein-Barr virus infection
ko05016 Huntington disease
ko03200 Viral proteins

ZFIN:

id description
ZDB-GENE-030410-3 Predicted to enable glutathione peroxidase activity and phospholipid-hydroperoxide glutathione peroxidase activity. Acts upstream of or within negative regulation of Wnt signaling pathway. Predicted to be active in mitochondrion and nucleus. Is expressed in several structures, including alar plate midbrain region; blastoderm; digestive system; musculature system; and visual system. Human ortholog(s) of this gene implicated in spondylometaphyseal dysplasia Sedaghatian type. Orthologous to human GPX4 (glutathione peroxidase 4).

Ensembl:

ensembl_id ENSDARG00000076836

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00033426 False 784 lncRNA 0.50 6 56642138 56655769
TCONS_00033130 False 879 mRNA 0.50 7 56642138 56655769
TCONS_00033131 True 647 mRNA 0.51 6 56642280 56649883

Neighbor

gene id symbol gene type direction distance location
XLOC_016968 pip5k1cb coding downstream 6356 56508451 ~ 56635782 (-)
XLOC_016967 ctxn1 coding downstream 210840 56430847 ~ 56431298 (-)
XLOC_016966 cers4b coding downstream 255097 56356652 ~ 56387041 (-)
XLOC_016965 uba52 coding downstream 293411 56339058 ~ 56348727 (-)
XLOC_016964 jund coding downstream 510826 56125174 ~ 56131312 (-)
XLOC_016970 arhgap45a coding upstream 23445 56679214 ~ 56757069 (-)
XLOC_016971 NA coding upstream 153523 56809292 ~ 56884888 (-)
XLOC_016972 NA coding upstream 397250 57053019 ~ 57061935 (-)
XLOC_016973 slc25a42 coding upstream 420310 57076079 ~ 57110477 (-)
XLOC_016974 dre-mir-7148 coding upstream 447632 57103401 ~ 57103485 (-)
XLOC_016963 NA non-coding downstream 546863 56060400 ~ 56095275 (-)
XLOC_016962 CU013534.1 non-coding downstream 599508 56042512 ~ 56042630 (-)
XLOC_016956 NA non-coding downstream 890440 55684668 ~ 55751698 (-)
XLOC_016955 NA non-coding downstream 978163 55639371 ~ 55663975 (-)
XLOC_016952 NA non-coding downstream 1417563 55215186 ~ 55224575 (-)
XLOC_016976 NA non-coding upstream 547242 57203011 ~ 57204446 (-)
XLOC_016979 si:ch1073-325m22.2 non-coding upstream 613012 57268781 ~ 57287258 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) G289329 NA non-coding CI01000075 null 1518990 ~ 1524862 (+)
rainbow trout (Oncorhynchus mykiss) G289421 NA non-coding NC_048567.1 CM023221.2 67591065 ~ 67591402 (-)