RNA id: TCONS_00003587


Basic Information

Item Value
RNA id TCONS_00003587
length 1518
RNA type mRNA
GC content 0.59
exon number 10
gene id XLOC_001788
representative False

Chromosome Information

Item Value
chromosome id NC_007121.7
NCBI id CM002894.2
chromosome length 45420867
location 573667 ~ 592860 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATGTCCATCACAAACACTCCCACCAGTAATGACGCGTGCCTGAGCATCGTGCACAGTCTGATGTGCCACCGGCAGGGCGGCGAGAGCGAGACCTTCGCCAAACGCGCCATCGAGAGCCTGGTGAAGAAGCTAAAGGAGAAGAAAGATGAGCTGGATTCTCTGATCACCGCTATCACCACTAACGGAGCGCATCCCAGCAAATGTGTGACCATACAGAGAACGCTGGACGGACggctgcagGTGGCGGGCCGGAAAGGATTCCCTCATGTGATTTATGCACGGTTATGGCGATGGCCTGATCTTCATAAGAACGAGCTGAAGCATGTCAAATACTGCCAGTTCGCCTTCGACCTGAAGTGTGACAGCGTGTGCGTCAACCCCTACCACTACGAGAGAGTGGTGTCTCCAGGAATAGATCTGTCTGGCCTCACACTGTCAGGCTCTGGTCCGTCAGGGCTGATGGTGAAGGATGAGTATGATTATGATGGGCCACCGTCTCTGCCTAGCACTGAGGGACACATGCAGACCATCCAGCACCCGCCGTCCCGCGCCGTCACCCAGGAGCCCTTCAGCACGCCCGCCCTGCTCCCGCCAGCAGAAGGCAGCAGCTCCGCCTCCAGCTCCGCCTTCTCCAGCATCGCCGTCGGATCCACAAATCCCACCTCCTCCTGGAGCAGGAACAGTAACTTCACCCCCAGCGTGCCTCATCATCAGAACGGGCATCTGCAGCATCACCCGCCCATGGCTCATCCGGCACACTACTGGCCTGTTCACAATGAAATCGCATTTCAGCCACCGATATCCAACCACCCTGCTCCTGAATACTGGTGCTCCATTGCCTACTTCGAGATGGACGTTCAGGTGGGCGAGACCTTCAAAGTGCCCTCGTCCTGCCCCATCGTGACGGTGGATGGGTACGTGGACCCGTCTGGAGGAGACAGATTCTGCCTCGGCCAGCTCAGCAACGTCCACAGAACAGAGGCCATCGAGAGAGCGAGACTGCACATCGGGAAGGGCGTCCAGCTGGAGTGTAAAGGTGAAGGAGACGTGTGGGTTCGCTGTCTGAGCGATCACGCGGTCTTCGTCCAGAGCTACTACCTGGACCGTGAGGCGGGACGCGCACCCGGGGACGCCGTGCACAAGATTTACCCCAGCGCATACATCAAGGTGTTTGACTTGCGTCAGTGCCACCGGCAGATGCAGCAGCAGGCAGCGACGGCTCAGGCAGCGGCAGCCGCTCAGGCAGCAGCAGTGGCCGGAAACATCCCCGGACCCGGATCTGTCGGAGGAATCGCTCCAGCTATCAGTTTGTCTGCGGCCGCTGGTATCGGTGTGGATGACCTGCGCCGGCTCTGTATCCTGCGCATGAGCTTCGTGAAGGGCTGGGGTCCCGATTACCCCCGGCAGAGCATTAAAGAGACGCCCTGCTGGATCGAGATCCATCTGCACCGTGCGCTGCAGCTGCTGGACGAGGTTCTGCACACCATGCCCATCGCAGACCCCACACCGttagactga

Function

GO:

id name namespace
GO:0007179 transforming growth factor beta receptor signaling pathway biological_process
GO:0048738 cardiac muscle tissue development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0007519 skeletal muscle tissue development biological_process
GO:0030154 cell differentiation biological_process
GO:0060395 SMAD protein signal transduction biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0048264 determination of ventral identity biological_process
GO:0030509 BMP signaling pathway biological_process
GO:0009653 anatomical structure morphogenesis biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0060026 convergent extension biological_process
GO:0071141 SMAD protein complex cellular_component
GO:0071144 heteromeric SMAD protein complex cellular_component
GO:0005634 nucleus cellular_component
GO:0005667 transcription regulator complex cellular_component
GO:0005737 cytoplasm cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0008134 transcription factor binding molecular_function
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific molecular_function
GO:0005515 protein binding molecular_function
GO:0003677 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:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0031625 ubiquitin protein ligase binding molecular_function
GO:0070411 I-SMAD binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-990603-8 Enables sequence-specific DNA binding activity. Contributes to transcription cis-regulatory region binding activity. Acts upstream of or within convergent extension; determination of ventral identity; and striated muscle tissue development. Located in nucleus. Part of SMAD protein complex. Is expressed in several structures, including digestive system; head; heart; immature eye; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in several diseases, including female reproductive organ cancer (multiple); hereditary hemorrhagic telangiectasia; juvenile polyposis syndrome; juvenile polyposis-hereditary hemorrhagic telangiectasia syndrome; and seminoma. Orthologous to human SMAD4 (SMAD family member 4).

Ensembl:

ensembl_id ENSDART00000129856

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00005663 lncRNA upstream 32340 541627 ~ 543589 (+) False XLOC_001786
TCONS_00005664 lncRNA upstream 32340 542855 ~ 543589 (+) True XLOC_001786
TCONS_00005794 lncRNA upstream 32866 540909 ~ 543063 (+) False XLOC_001786
TCONS_00005797 lncRNA downstream 1176 590604 ~ 592860 (+) True XLOC_001788
TCONS_00005798 lncRNA downstream 144359 733787 ~ 793309 (+) False XLOC_001789
TCONS_00005799 lncRNA downstream 144376 733804 ~ 796894 (+) False XLOC_001789
TCONS_00005800 lncRNA downstream 187913 777341 ~ 793309 (+) False XLOC_001789
TCONS_00005665 lncRNA downstream 196310 785738 ~ 793388 (+) False XLOC_001789
TCONS_00003585 mRNA upstream 9322 563252 ~ 566607 (+) True XLOC_001787
TCONS_00003584 mRNA upstream 43301 518546 ~ 532628 (+) True XLOC_001785
TCONS_00003582 mRNA upstream 63623 506538 ~ 512306 (+) False XLOC_001784
TCONS_00003581 mRNA upstream 70559 466926 ~ 505370 (+) True XLOC_001783
TCONS_00003580 mRNA upstream 121307 453619 ~ 454622 (+) True XLOC_001782
TCONS_00003589 mRNA downstream 73 589501 ~ 591847 (+) False XLOC_001788
TCONS_00003591 mRNA downstream 463163 1052591 ~ 1107558 (+) True XLOC_001792
TCONS_00003592 mRNA downstream 807512 1396940 ~ 1414161 (+) True XLOC_001793
TCONS_00003593 mRNA downstream 1001176 1590604 ~ 1591103 (+) True XLOC_001795
TCONS_00003596 mRNA downstream 1049448 1638876 ~ 1675351 (+) False XLOC_001796
TCONS_00003583 other upstream 68673 506563 ~ 507256 (+) True XLOC_001784
TCONS_00003569 other upstream 363982 211782 ~ 211947 (+) True XLOC_001770
TCONS_00003590 other downstream 215816 805244 ~ 805359 (+) True XLOC_001790
TCONS_00003597 other downstream 1075494 1664922 ~ 1665038 (+) True XLOC_001797
TCONS_00003605 other downstream 1586155 2175583 ~ 2267357 (+) False XLOC_001805
TCONS_00003616 other downstream 2099137 2688565 ~ 2688681 (+) True XLOC_001815
TCONS_00003633 other downstream 2395616 2985044 ~ 3026523 (+) True XLOC_001822

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) TU444767 True 2827 lncRNA 0.49 10 CI01000203 470428 ~ 478233 (-)