RNA id: TCONS_00007918


Basic Information

Item Value
RNA id TCONS_00007918
length 1942
RNA type mRNA
GC content 0.46
exon number 3
gene id XLOC_004145
representative False

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 25251495 ~ 25257595 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GCGGGTCCAAATGGACGTAAACCCACTTACTAGACTGTCAggctattttaaataagtacaggCTCACTAATTGTAGTGCATTTCACATCAGCGTTCACGTTACGAGAAGCACGGATTGGATCGTCGTTGCATTTCTGGGACTATCTGAGAGTGGAGGATTTAGTTTTTCCATCACTGAAAGTAACTGGAGTGGACTGATCAACTTCAGAGTTCAGCATGCCTCGGTCTTTCCTGGTAAAGAAGTATTTCACCAGCAAGAGGCCAAACTACAGCGAGCTGGAATGTCAGAACGACACTTCACCAGACAGATACCCGCTAGCAGAGCTTCCAGCAGTCAGCAATGACTTCCCAGTGACGTGTTTGACCACCGGACTGGTCTGGGACGTCAGCTTGCTACCTTCCCTTCACAATTCCCCATCCCCGTCCACCCTCTCCACAAACCAGGGCCCGCTGGACCTCAGCTCCCCATCCAGCATCAGCTGCAGCAGCAGTGGGGAAGAAGATGAAGGACGGACGTCAGACCCACCAAGCCCAGATTCCTCTGACACCTATCACCCCCAGCAAACTAGCAGGCCGCGACGCTCCAACAAGAGCAGGGCTGGACAGAGAGAGGACAAGAGCGAGGCTGCAGTTACTGCCGCCAGTCGACCAGCCTTCTTCTGCAAGCACTGTCCTAAAGAGTACAACAGCCTCGGGGCGCTGAAGATGCACATCCGCTCCCACACACTGCCCTGCGTCTGTCCCACCTGCGGAAAGGCCTTCTCCAGACCCTGGCTGCTGAGGGGacacattcgcacacatacagGTGAGCGTCCGTTCTCCTGCCCACACTGTAACCGTGCCTTCGCAGACCGCTCGAACCTCCGCGCGCACCTGCAGACCCACGCAGATGTGAAGAAATACCAGTGCAGCACCTGCTCTCGCACCTTCAGTCGCATGTCACTGCTGCAGAAACACAGCGCGGCCGGTTGCTGTCCCTCCACGGCCAATGTCCAATAGCCATTTTATTCTAATTCAGGACTAATGAGAAAAGCTTCTTCTCTAAACGGGCACAATATTCAACAGAAGGATGACGCATCATTAAAGCGGACTTCTTAAAACATTTCCAAATGCCTTTTTCCTCGAACCAAAATACTTCAGATGAAGGAATTATGAATGTTAAGGGTGTCCTGAAGCAGCTGCTGTCAGGTTGGGGGTGGGTTGACTATGGTAGGGTATGTCTCTcagcatgacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacagacagagacagCTGTTGTGTGGTGCGGAGGCAGTGTGCTAACAGGTGCCCTGACCGCCACATCTCTGAAAACAGGTGGCGTCTGCTGATTTCTCTGGAAACACACTTGGAGAGAGTCCTTATGGAGCACAGTTGACTGCTTTActtttttttgatgttgttgGTTTTAAAGTTTTGTAGCTTGCATGCGGAAGGTGCatcgcatgttttttttttttccaataattcTTTTCACCaaagattgttttttttactctgtctattgttctttttttgtacAGTTTTAAGTGCACTCCAATTTACCAAAGAGTATTGAAGTCCATTCATTTTGTATTATATCGAGTGATTGGACCATTGAAACCAAAGCCATgctttttcttttgtgtgtgtgtaatttaaagaGTTTTGAGACACTTCTGAATTTGTGAGGAAACGGACATTCTTATTAAACAACTACCAAATTTTATACACCTATCTATATTCCATCAACTTTTCGTCACATTTTATTGATGCCAGAATTTGTGCATAAAGTGTTTTCTTAAAACCGAATGAGTTCAGTGCAAtttttagcattttgtttttcttatttcttttgtatttgtccaaatcatttccattcaataaaataatttaagtttatacAAA

Function

GO:

id name namespace
GO:0042074 cell migration involved in gastrulation biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0001837 epithelial to mesenchymal transition biological_process
GO:0009953 dorsal/ventral pattern formation biological_process
GO:0007369 gastrulation biological_process
GO:0008078 mesodermal cell migration biological_process
GO:0005634 nucleus cellular_component
GO:0046872 metal ion binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:0008270 zinc ion binding molecular_function
GO:0051059 NF-kappaB binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-990415-255 Enables NF-kappaB binding activity. Acts upstream of or within ameboidal-type cell migration; dorsal/ventral pattern formation; and epithelial to mesenchymal transition. Located in nucleus. Is expressed in several structures, including blastodisc; germ ring; mesoderm; pharyngeal arch; and presumptive mesoderm. Orthologous to human SNAI1 (snail family transcriptional repressor 1).

Ensembl:

ensembl_id ENSDART00000130477

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00007917 lncRNA downstream 38231 25209734 ~ 25213264 (-) True XLOC_004143
TCONS_00007912 lncRNA downstream 431494 24819265 ~ 24820001 (-) True XLOC_004141
TCONS_00008472 lncRNA downstream 537202 24712969 ~ 24714293 (-) True XLOC_004140
TCONS_00008795 lncRNA downstream 537220 24711119 ~ 24714275 (-) False XLOC_004140
TCONS_00008471 lncRNA downstream 538573 24711804 ~ 24712922 (-) False XLOC_004140
TCONS_00008796 lncRNA upstream 111067 25368112 ~ 25403683 (-) False XLOC_004147
TCONS_00007921 lncRNA upstream 111067 25368112 ~ 25408896 (-) False XLOC_004147
TCONS_00007924 lncRNA upstream 155298 25412343 ~ 25413153 (-) True XLOC_004148
TCONS_00008797 lncRNA upstream 218260 25475305 ~ 25476582 (-) False XLOC_004150
TCONS_00008798 lncRNA upstream 218260 25475305 ~ 25476980 (-) False XLOC_004150
TCONS_00007914 mRNA downstream 37806 25181886 ~ 25213689 (-) False XLOC_004143
TCONS_00007915 mRNA downstream 37844 25182813 ~ 25213651 (-) False XLOC_004143
TCONS_00007911 mRNA downstream 570203 24671676 ~ 24681292 (-) True XLOC_004139
TCONS_00007907 mRNA downstream 712635 24464356 ~ 24538860 (-) False XLOC_004138
TCONS_00007908 mRNA downstream 712643 24465292 ~ 24538852 (-) False XLOC_004138
TCONS_00007920 mRNA upstream 56765 25313810 ~ 25324534 (-) True XLOC_004146
TCONS_00007922 mRNA upstream 125557 25382602 ~ 25384213 (-) True XLOC_004147
TCONS_00007923 mRNA upstream 154869 25411914 ~ 25418856 (-) False XLOC_004148
TCONS_00007925 mRNA upstream 179395 25436440 ~ 25461336 (-) True XLOC_004149
TCONS_00007929 mRNA upstream 272003 25529048 ~ 25538341 (-) False XLOC_004151
TCONS_00007916 other downstream 46252 25205153 ~ 25205243 (-) True XLOC_004144
TCONS_00007913 other downstream 283608 24967771 ~ 24967887 (-) True XLOC_004142
TCONS_00007910 other downstream 718537 24525676 ~ 24532958 (-) True XLOC_004138
TCONS_00007888 other downstream 1596017 23655350 ~ 23655478 (-) True XLOC_004130
TCONS_00007873 other downstream 2092188 23159189 ~ 23159307 (-) True XLOC_004123
TCONS_00007927 other upstream 219054 25476099 ~ 25476185 (-) True XLOC_004150
TCONS_00007928 other upstream 271512 25528557 ~ 25532480 (-) False XLOC_004151
TCONS_00007931 other upstream 412794 25669839 ~ 25669955 (-) True XLOC_004152
TCONS_00007940 other upstream 600896 25857941 ~ 25931082 (-) False XLOC_004157
TCONS_00007943 other upstream 763054 26020099 ~ 26180714 (-) True XLOC_004157

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000306_02966994_02968675.mRNA True 2339 mRNA 0.44 3 CI01000306 2965937 ~ 2969186 (-)