XLOC_003139


Basic Information

Item Value
gene id XLOC_003139
gene name NA
gene type non-coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 2198530 ~ 2205798 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00008512
GGTGGAAAATTTACAGCTATGTAATAAAAGTTTATGACTAAACCAAGGATTGGATTGGCTGTGCTAAGTCACATGGTGTCCTCTCCATGATAATGAACTTTATACTGTTGTCTCTGGCTCAATCATATGCGTTCCCCATCAGGCTGAACACGGAACATTCAGTTTTTAGTCTTTCGATTGCAATAGCTACTGTAATATTTTATTGACAACTGTTTTTCAATCTTCATTACCTCTCTCATCGCGTTTAGTTTTCACAGATTAGGAAAGAAATGGTAGAAGACTAACCTACATTAGTAAGAATGTATGTACACTAAGACGAGAACGTTGTCTTTGCTGTGAAGGAAAAAGAAATGGATGTTCGCTTTGGATTACCGCAGCTAATTCTGAAGCTCTTGCAATTACCTCCCACCCTTTCCTCAGGAGCTGAAGATCTCTCAAAACGCGTCACAAGAGAAATGTGTTAAGATATGATTTGGAACTATGTTGTAAGTATTTATTTAACCAAACTATTCATGGATTTACTGCTGTTTAGTATTTTACAAGCAATGTGTGTTTACGACTTTTAGCTGGCATTTGCCGTCTCATTGAACTATTGCAAACAACTGATTCGGATGTGGCACTCTATTGAATGGGTTGTTATCTGATTGTAAAATGCCTTAAGCCGCCAAAGACAACTGCAATAAAAACACATTCCTGCAC
>TCONS_00008379
ACACGGAACATTCAGTTTTTAGTCTTTCGATTGCAATAGCTACTGTAATATTTTATTGACAACTGTTTTTCAATCTTCATTACCTCTCTCATCGCGTTTAGTTTTCACAGATTAGGAAAGAAATGGTAGAAGACTAACCTACATTAGTAAGAATGTATGTACACTAAGACGAGAACGTTGTCTTTGCTGTGAAGGAAAAAGAAATGGATGTTCGCTTTGGATTACCGCAGCTAATTCTGAAGCTCTTGCAATTACCTCCCACCCTTTCCTCAGGAGCTGAAGATCTCTCAAAACGCGTCACAAGAGAAATGTGTTAAGATATGTGAACGAATCATCATTGACCTCCATGCAACTGGAAGAAACGAATAAAGGACAGACCGTCGACAAATGTGAAGCCTGCAGTTGATACTTTAAATTGTCATCTAATTCCGAAAAATATACATGAAAATGTAGCATTCCCGAAAGATGATTGATCCACAGAAACATCGTACCACACACATATGCATTTGAGAATAAACCTCGAGCTCTGTTTCATGTTCAGTTTGGAGGATTGTTCAAAGTTAAATCTAATTAAATTGAATAAGCGAAAATAAAGCTATACTGGACAACCACACTTGAGGCACG
>TCONS_00006200
GTATGTACACTAAGACGAGAACGTTGTCTTTGCTGTGAAGGAAAAAGAAATGGATGTTCGCTTTGGATTACCGCAGCTAATTCTGAAGCTCTTGCAATTACCTCCCACCCTTTCCTCAGGAGCTGAAGATCTCTCAAAACGCGTCACAAGAGAAATGTGTTAAGATATGATTTAAACAGCGGTCAAGAAGTTCTACCCAGCGTTGCCATCAGCTCGACAAACTATGACCCGGTGCGACATTTTTCGCCATATGGCGCCGCCGTTGCCCAAAACCGGATATACTCCAATCCGTTCTATTCACACCAAGAAAACGTTATGTTTGGGTCAAGCCGACCGTACGATTACGGATCAAATATGTTCTACCAGGACAAAGATGTGCTTCCAAGTTGCAGGCAAGGCTTTGGGCAAACACAGGGTTCATTGACGCAGGATTACGCTTCAGACCAAGGCAAGACTATGGAACCGAAAGGAAGTGTTCAAATATATCCATGGATGCAGCGGATGAACTCGCATAGTGGAGTTGGCTATGGGTCTGACAGACGGCGAGGTCGCCAAATCTATTCGCGATACCAAACTTTAGAACTTGAGAAAGAATTTCATTACAATCGCTATTTGACAAGACGCAGACGAATTGAGATTGCCAACACATTGTGTCTGTCGGAACGCCAGATTAAAATTTGGTTTCAGAACCGCCGGATGAAATGGAAGAAGGAGAGCAATCTCACGTCCATCCTCAATGACAATGGCTCGGTAGGAGCTGGCCAAGACACGGACAAAGAAGAAACAGGGGAAACCGCCGAAAAAGATGAGCATGACTGATTGACTTACTAACTAATTAAAAGACATTCCGTTTGAAAACGTTCTTACATAACTAAGCTACCTATGGAATTTACACAATTTGCACAATTAAAACCAAAAACTGTTACAATTCCTTTAGATGCAAAGCGTGTGTTGCTTCGCCACTTATTTCACTATGATTCTGAAAAGCTGTTTATCCAGAGCAATTTAATTCATAAATCAGTGCTCTGACTGAAAATGTTTTACCTATCTTGTGTGATTTAATCTTGTCATTAAACATCTTATTTGTTCTGATGTACTCTGAAGTGCAAATAAGGGACTGTTGATGTAGACCAAATATGAAAATTCCAAATATTAAACTACAATCATTTCTTCTGGTCCTAGGAAGTGCATTGTACATGTTTGTAAATATGAGATTCAAATACTTTTGATGAGCATTTGTTTAGATTGACGTactgttttgtgttttttctttacTTTGTGATGCGTTCTGGGAGAACCACATACGTTGTAAAAAGTATCCTTCATTACTCTTTTTTTCCAAATGTTGAATTTTAGCAAAAAAGCAAGATAATAAAATGTTCGAACATTTACGCAATAAAGTTGTAATCAATATAACAAT
>TCONS_00006201
GGGAAGAGAGGCCtaggaaaaaaaaagtgttgttttttaaAGAAGAAGGGATGAATTCCTATTTTACGAACCCATCGCTGTCGTGTCATTTAAACAGCGGTCAAGAAGTTCTACCCAGCGTTGCCATCAGCTCGACAAACTATGACCCGGTGCGACATTTTTCGCCATATGGCGCCGCCGTTGCCCAAAACCGGATATACTCCAATCCGTTCTATTCACACCAAGAAAACGTTATGTTTGGGTCAAGCCGACCGTACGATTACGGATCAAATATGTTCTACCAGGACAAAGATGTGCTTCCAAGTTGCAGGCAAGGCTTTGGGCAAACACAGGGTTCATTGACGCAGGATTACGCTTCAGACCAAGGCAAGACTATGGAACCGAAAGGAAGTGTTCAAATATATCCATGGATGCAGCGGATGAACTCGCATAGTGGAGTTGGCTATGGGTCTGACAGACGGCGAGGTCGCCAAATCTATTCGCGATACCAAACTTTAGAACTTGAGAAAGAATTTCATTACAATCGCTATTTGACAAGACGCAGACGAATTGAGATTGCCAACACATTGTGTCTGTCGGAACGCCAGATTAAAATTTGGTTTCAGAACCGCCGGATGAAATGGAAGAAGGAGAGCAATCTCACGTCCATCCTCAATGACAATGGCTCGGTAGGAGCTGGCCAAGACACGGACAAAGAAGAAACAGGGGAAACCGCCGAAAAAGATGAGCATGACTGATTGACTTACTAACTAATTAAAAGACATTCCGTTTGAAAACGTTCTTACATAACTAAGCTACCTATGGAATTTACACAATTTGCACAATTAAAACCAAAAACTGTTACAATTCCTTTAGATGCAAAGCGTGTGTTGCTTCGCCACTTATTTCACTATGATTCTGAAAAGCTGTTTATCCAGAGCAATTTAATTCATAAATCAGTGCTCTGACTGAAAATGTTTTACCTATCTTGTGTGATTTAATCTTGTCATTAAACATCTTATTTGTTCTGATGTACTCTGAAGTGCAAATAAGGGACTGTTGATGTAGACCAAATATGAAAATTCCAAATATTAAACTACAATCATTTCTTCTGGTCCTAGGAAGTGCATTGTACATGTTTGTAAATAT
>TCONS_00006202
GGGAAGAGAGGCCtaggaaaaaaaaagtgttgttttttaaAGAAGAAGGGATGAATTCCTATTTTACGAACCCATCGCTGTCGTGTCATTTAAACAGCGGTCAAGAAGTTCTACCCAGCGTTGCCATCAGCTCGACAAACTATGACCCGGTGCGACATTTTTCGCCATATGGCGCCGCCGTTGCCCAAAACCGGATATACTCCAATCCGTTCTATTCACACCAAGAAAACGTTATGTTTGGGTCAAGCCGACCGTACGATTACGGATCAAATATGTTCTACCAGGACAAAGATGTGCTTCCAAGTTGCAGGCAAGGCTTTGGGCAAACACAGGGTTCATTGACGCAGGATTACGCTTCAGACCAAGGCAAGACTATGGAACCGAAAGGAAGTGTTCAAATATATCCATGGATGCAGCGGATGAACTCGCATAGAGTTGGCTATGGGTCTGACAGACGGCGAGGTCGCCAAATCTATTCGCGATACCAAACTTTAGAACTTGAGAAAGAATTTCATTACAATCGCTATTTGACAAGACGCAGACGAATTGAGATTGCCAACACATTGTGTCTGTCGGAACGCCAGATTAAAATTTGGTTTCAGAACCGCCGGATGAAATGGAAGAAGGAGAGCAATCTCACGTCCATCCTCAATGACAATGGCTCGGTAGGAGCTGGCCAAGACACGGACAAAGAAGAAACAGGGGAAACCGCCGAAAAAGATGAGCATGACTGATTGACTTACTAACTAATTAAAAGACATTCCGTTTGAAAACGTTCTTACATAACTAAGCTACCTATGGAATTTACACAATTTGCACAATTAAAACCAAAAACTGTTACAATTCCTTTAGATGCAAAGCGTGTGTTGCTTCGCCACTTATTTCACTATGATTCTGAAAAGCTGTTTATCCAGAGCAATTTAATTCATAAATCAGTGCTCTGACTGAAAATGTTTTACCTATCTTGTGTGATTTAATCTTGTCATTAAACATCTTATTTGTTCTGATGTACTCTGAAGTGCAAATAAGGGACTGTTGATGTAGACCAAATATGAAAATTCCAAATATTAAACTACAATCATTTCTTCTGGTCCTAGGAAGTGCATTGTACATGTTTGTAAATATGAGATTCAAATACTTTTGATGAGCATTTGTTTAGATTGACGTactgttttgtgttttttctttacTTTGTGATGCGTTCTGGGAGAACCACATACGTTGTAAAAAGTATCCTTCATTACTCTTTTTTTCCAAATGTTGAATTTTAGCAAAAAAGCAAGATAATAAAATGTTCGAACATTTACGCAATAAAGTTGTAATCAATATAACAAT

Function

GO:

id name namespace
GO:0048729 tissue morphogenesis biological_process
GO:0042692 muscle cell differentiation biological_process
GO:0048731 system development biological_process
GO:0048732 gland development biological_process
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0016070 RNA metabolic process biological_process
GO:0048468 cell development biological_process
GO:0035239 tube morphogenesis biological_process
GO:0048747 muscle fiber development biological_process
GO:0021546 rhombomere development biological_process
GO:0051146 striated muscle cell differentiation biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0002009 morphogenesis of an epithelium biological_process
GO:0018130 heterocycle biosynthetic process biological_process
GO:0006351 transcription, DNA-templated biological_process
GO:0065007 biological regulation biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0043009 chordate embryonic development biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0030154 cell differentiation biological_process
GO:0048513 animal organ development biological_process
GO:1990399 epithelium regeneration biological_process
GO:0055001 muscle cell development biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0071599 otic vesicle development biological_process
GO:0021593 rhombomere morphogenesis biological_process
GO:0035295 tube development biological_process
GO:0009058 biosynthetic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:0009611 response to wounding biological_process
GO:1901576 organic substance biosynthetic process biological_process
GO:0009887 animal organ morphogenesis biological_process
GO:0007275 multicellular organism development biological_process
GO:0009888 tissue development biological_process
GO:0009889 regulation of biosynthetic process biological_process
GO:0097659 nucleic acid-templated transcription biological_process
GO:0031323 regulation of cellular metabolic process biological_process
GO:0060429 epithelium development biological_process
GO:0031326 regulation of cellular biosynthetic process biological_process
GO:0048562 embryonic organ morphogenesis biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0048568 embryonic organ development biological_process
GO:0009653 anatomical structure morphogenesis biological_process
GO:0048856 anatomical structure development biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:0006725 cellular aromatic compound metabolic process biological_process
GO:0048589 developmental growth biological_process
GO:1901360 organic cyclic compound metabolic process biological_process
GO:1903506 regulation of nucleic acid-templated transcription biological_process
GO:0048596 embryonic camera-type eye morphogenesis biological_process
GO:1901362 organic cyclic compound biosynthetic process biological_process
GO:0048598 embryonic morphogenesis biological_process
GO:0010467 gene expression biological_process
GO:0031076 embryonic camera-type eye development biological_process
GO:0010468 regulation of gene expression biological_process
GO:0048869 cellular developmental process biological_process
GO:0042246 tissue regeneration biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0031099 regeneration biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0040007 growth biological_process
GO:0070654 sensory epithelium regeneration biological_process
GO:0048646 anatomical structure formation involved in morphogenesis biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0003002 regionalization biological_process
GO:0007389 pattern specification process biological_process
GO:0048048 embryonic eye morphogenesis biological_process
GO:0050794 regulation of cellular process biological_process
GO:0007399 nervous system development biological_process
GO:0061061 muscle structure development biological_process
GO:0032501 multicellular organismal process biological_process
GO:2001141 regulation of RNA biosynthetic process biological_process
GO:0032502 developmental process biological_process
GO:0060537 muscle tissue development biological_process
GO:0032774 RNA biosynthetic process biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0019438 aromatic compound biosynthetic process biological_process
GO:0007417 central nervous system development biological_process
GO:0010556 regulation of macromolecule biosynthetic process biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0007420 brain development biological_process
GO:0014706 striated muscle tissue development biological_process
GO:0030900 forebrain development biological_process
GO:0034654 nucleobase-containing compound biosynthetic process biological_process
GO:2000112 regulation of cellular macromolecule biosynthetic process biological_process
GO:0060562 epithelial tube morphogenesis biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0007166 cell surface receptor signaling pathway biological_process
GO:0060322 head development biological_process
GO:0042060 wound healing biological_process
GO:0009790 embryo development biological_process
GO:0009792 embryo development ending in birth or egg hatching biological_process
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003690 double-stranded DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000976 transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:0000987 cis-regulatory region sequence-specific DNA binding molecular_function
GO:0140110 transcription regulator activity molecular_function
GO:0001067 regulatory region nucleic acid binding molecular_function
GO:1990837 sequence-specific double-stranded DNA binding molecular_function

KEGG:

id description
ko03230 Viral genome structure
ko05164 Influenza A
ko03200 Viral proteins

ZFIN:

id description
ZDB-GENE-000822-1 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in several structures, including margin; musculature system; neuroectoderm; paraxial mesoderm; and tail bud. Orthologous to human HOXC6 (homeobox C6).

Ensembl:

ensembl_id ENSDARG00000101954

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00008512 False 699 lncRNA 0.38 2 2198530 2200893
TCONS_00008379 False 624 lncRNA 0.38 2 2198677 2205798
TCONS_00006200 False 1420 mRNA 0.40 3 2198831 2204754
TCONS_00006201 False 1128 lncRNA 0.41 2 2202987 2204544
TCONS_00006202 True 1335 mRNA 0.39 2 2202987 2204754

Neighbor

gene id symbol gene type direction distance location
XLOC_003138 mir196c coding upstream 7800 2190621 ~ 2190730 (+)
XLOC_003137 hoxc11b coding upstream 13356 2180072 ~ 2185174 (+)
XLOC_003136 hoxc12b coding upstream 23497 2172335 ~ 2175033 (+)
XLOC_003135 hoxc13b coding upstream 35709 2156430 ~ 2162821 (+)
XLOC_003134 rargb coding upstream 102061 2089461 ~ 2096469 (+)
XLOC_003140 NA coding downstream 102411 2308209 ~ 2320355 (+)
XLOC_003141 igfbp6a coding downstream 185671 2391469 ~ 2397974 (+)
XLOC_003142 pip4k2cb coding downstream 193045 2398843 ~ 2413107 (+)
XLOC_003143 ube2v1 coding downstream 210266 2416064 ~ 2429303 (+)
XLOC_003144 csnk2a4 coding downstream 228464 2434262 ~ 2446346 (+)
XLOC_003250 BX324177.11 misc downstream 9140005 11345803 ~ 11346099 (+)
XLOC_003255 BX324177.14 misc downstream 9167088 11372886 ~ 11373182 (+)
XLOC_003257 BX324177.13 misc downstream 9180564 11386362 ~ 11386658 (+)
XLOC_003260 BX324177.2 misc downstream 9212235 11418033 ~ 11418323 (+)
XLOC_003262 BX324177.15 misc downstream 9223595 11429393 ~ 11429689 (+)
XLOC_003132 NA non-coding upstream 201120 1935684 ~ 1997410 (+)
XLOC_003133 NA non-coding upstream 245936 1951631 ~ 1952594 (+)
XLOC_003126 AL935272.1 non-coding upstream 652299 1546117 ~ 1546231 (+)
XLOC_003118 FQ311892.1 non-coding upstream 1467607 730807 ~ 730923 (+)
XLOC_003149 FQ790208.1 non-coding downstream 409272 2615070 ~ 2616023 (+)
XLOC_003156 CT583672.1 non-coding downstream 621755 2827553 ~ 2828675 (+)
XLOC_003159 dre-mir-724 non-coding downstream 970888 3176686 ~ 3176770 (+)
XLOC_003160 NA non-coding downstream 997689 3203487 ~ 3206698 (+)

Expression


Co-expression Network