RNA id: TCONS_00009252


Basic Information

Item Value
RNA id TCONS_00009252
length 3210
RNA type mRNA
GC content 0.46
exon number 12
gene id XLOC_004672
representative True

Chromosome Information

Item Value
chromosome id NC_007123.7
NCBI id CM002896.2
chromosome length 49182954
location 19958845 ~ 19975373 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

TGCATTAGTTCTGTTTGTGTGCTCTAACTGCTAGATATAAGTTAAACAGCACGTTTATTCCTCGTCTCGTCCTGTTAAAAGCCAATAGATGGTGATGATGAGCTGAATGTATTAAGAAAACTAAACACAATGAAGTATCATTTCAGTAGGTGAGATCTGGATGATTTGGGTCAGTCGTTGGTGAATTGAGCCGGTGCTGGTGAAGATGGCGAGTGCTCTGCTGGAGTATGAGACGGAGATGTTTCTGAGTGTGTTCAGCACAGACGGGCTGCTGATCACGGCTGAAGGACTCGGCATTGACCGCCTTCTGCTGCACTTCATGAAGGTGTATTCTGAGGAGGGCAGCTTGGTGCTCTTGCTGAACACCAGCACTCCTGAACAGGAGTATTTGACGGAGCGGCTGCGAGCTGAAGGAGTCACTCATCTTCCTCAAACTGTGACCAGTGATGTGCAGAGTGCTGACAGATATAACGTGTACACTAAAGGAGGAGTGCTGTTTGTCACTAGCCGAATCCTAGTGGTGGATTTCCTGACTGACAGAATCCCTGCTCACCTAGTAACAGGAATCCTGGTGTACCGGGCACATAATATCATTGAGTCTTGTCAGGAGGCTTTCATTTTGAGACTTTATCGTCAGAAAAACAAAACCGGCTTCATCAAGGCCTTTACAGATAAAGCCACATCCTTCTCTTCAGGATTCTGTAAAGTCGAGCGTGTCATGAGAAACTTGTTTGTGAAGAAACTTTTTCTCTGGCCAAGATTCCAAGCATCAGTGAACGCAACGCTGGATAAACACAAGCCAGATGTGGTGGAGCTGCACGTGACTCTGACTCCAGCAATGAGAGCCATTCAGAGCTCCATTCTGGACATCATGAATGCCTGCCTGAAAGAGCTGAAGCGCTACAACCCCACACTGGAAGCAGAAGACCTTTCTTTGGAGAACAGCCTGGGCACTGCCTTTGAGAAAACAATTCGTCATTACCTTGACCCACTGTGGCATCAGCTGGGGTCCAGGACCAAATCTCTTGTTCAGGACCTGAAGATTTTAAGAACCCTTCTTCTCTACCTCACTCAGTACGACTGTGTCACCTTCCTCAATCTGCTGGAGTCTTTGAGAACCAGCCAGAAAAGTTTTGGTAGTAATTCAGGTTGGTTGTTCCTGGACTCAAGCATGTCTATGTTTGTAAATGCTCGCAGTCGTGTGTATCGCATTCAGGAGTCTAAGAAAAAACTGAAAGTTGGAGAGATTGAGCAGAAACAAAACCTAGCGCCTCCGAAAAGAGAGCTTGTGCTTGAGAAGAATCCAAAGTGGGAAGCACTTACAGAAGTCCTACAGGAGATTGAGAAAGAAAACAGCAAATCTGAGCACGAACcagGCCGAGTGTTGATATGTGCCAGTGATGACAGAACCTGTGCTCAGCTGAAGGAATACATCCAAAAAGGGCCAGAACACCTGCTGAACCGCCTTTATTCACGCACTATTGGAAAAGAAGATCCTCAGCCTGATTTACTGAAGCTTGACAAAGGCTGGCAAAAGAAAGACTCTGCTAGGAGCAAAGGAAAAAACTGCCGTCAGAAAAGAACCAAAGCCAACTCAAAGAAACCGGCAAAGATGGAGAAACTGTCAAGAGTCTCTCAGGACGATAGTGCTGATAAGGACCTTAATGAGAACAGTGAAGATGAAGGAGGGTTGAttgaagaggaggaagaagaggagatTGTTCTGGATCTATCATCTGATGATTATTATGGTATTCTGAAAGAGCCACTGACTGTCATTCACCCACTGAAGGGATGCAGTGACCCCTACAGTCTGACCCGCGTGCTGCATGAGGTTGACCCCATGTTTGTCGTCTTGTACGATGCTGAACTCAGTTTTGTGCGGCAGCTGGAGATTTATAAAGCATGCAGGCCTGGAAAACCACTCCGTGTGTATTTTCTCATATATGGAGGTTCAACAGAAGAACAGAGATATCTTACAGCATTAAACAAAGAAAAGCAAGCGTTTGAGCACCTCATAAGGGAAAAGGCCAGCATGGTTGTGCCAGAAGAAAGAGAAGGTAGAGAAGACACCAATCTAGATCTTGTCCGCAGTCAGGAACCTGCTAGTGCCGCCACAAACACCCGCAAAGCAGGGGGACTTGAAGAGGTTAAAGAGCCTCATCGGATCATCGTCGACATGAGAGAGTTTCGCAGTGAACTTCCTTCACTTCTGCATCGACGTGGTCTGGACATCGAGCCTGTCACCTTAGAGGTCGGCGACTACATACTGACGTCTGACATCTGCGTAGAGCGCAAAAGCGTCAGCGACCTCATTGGCTCCTTACAGAGCGGACGCCTTTACACACAGTGCCTCTCCATGACTCGATTCTACCGCCGTCCTGTGTTGCTCATCGAGTTTGACCCCGCTAAACCATTCTCCCTGGTGGCCCGCAGTGACTTTCGGCAGGAGATCTCAGCCAACGATGTCACCTCCAAACTGACCCTTCTCACCCTCCATTTCCCCCGCCTTAGGCTCCTCTGGTGCCCTTCGCCGTATGTGACGGCAGAGCTGTTTCAGGAGCTCAAGCATGGCCGTACCGAGCCGGACGCCAGCACAGCTCAGGCAGTTACAGCAGAATCAGAGACTGTGACCGAATCTGCAGATCTGTACAATCCTGGACCTTACGACTTCCTGCTGCGTATGCCTGGAGTCAATGTGAAGAACTTCAAGAGTCTGATAAAACATGTTTCCTGCCTCGCTGATCTTGTGACATTTAGCCAGGAGACGCTCAGTGAGATTTTGGGCAGCAGCAGCAATGCCAGGATGCTTTATGAATTCATACACAATCCTATGGATGTGCGGCCAATTCAGAAGAATAAGTAGATATCGTGAGGagaaataaaaagtgtttttattgtgaTATTGTGGGCCAATCGTGGAAATTGTACCTTGATAAAagggtttatttttatatttattgtaaaattaagatgcagtgaatgaattaatgtatttctgaatatttaaatgccttgtattttttaaatgttgtgttaGAATTCGTAGGTTTGGTGTGACTTTGCATGTAGTTATAGATGTTCATTGTAGATAACTTTACTAACTGTACTGTAGAGTCATTGGCTTAGAAGGTGAGTTTCATATCACCACtcttttagaaaaatgttgcaaTTTTTATCGTGATTGAAATAAACTATTTCTGTAATGAA

Function

GO:

id name namespace
GO:1901255 nucleotide-excision repair involved in interstrand cross-link repair biological_process
GO:0000712 resolution of meiotic recombination intermediates biological_process
GO:0000724 double-strand break repair via homologous recombination biological_process
GO:0006281 DNA repair biological_process
GO:0006296 nucleotide-excision repair, DNA incision, 5'-to lesion biological_process
GO:0000110 nucleotide-excision repair factor 1 complex cellular_component
GO:0000014 single-stranded DNA endodeoxyribonuclease activity molecular_function
GO:0004518 nuclease activity molecular_function
GO:0004520 endodeoxyribonuclease activity molecular_function
GO:0003677 DNA binding molecular_function
GO:0003684 damaged DNA binding molecular_function
GO:0003697 single-stranded DNA binding molecular_function

KEGG:

id description
ko03420 Nucleotide excision repair
ko03460 Fanconi anemia pathway
ko03032 DNA replication proteins
ko03400 DNA repair and recombination proteins

ZFIN:

id description
ZDB-GENE-030131-5533 Predicted to enable damaged DNA binding activity; single-stranded DNA binding activity; and single-stranded DNA endodeoxyribonuclease activity. Predicted to be involved in DNA metabolic process. Predicted to act upstream of or within DNA repair. Predicted to be part of nucleotide-excision repair factor 1 complex. Is expressed in liver. Human ortholog(s) of this gene implicated in Fanconi anemia complementation group Q; XFE progeroid syndrome; pancreatic cancer; xeroderma pigmentosum; and xeroderma pigmentosum group F. Orthologous to human ERCC4 (ERCC excision repair 4, endonuclease catalytic subunit).

Ensembl:

ensembl_id ENSDART00000015780

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00010733 lncRNA upstream 499752 19458809 ~ 19459285 (+) True XLOC_004670
TCONS_00009244 lncRNA upstream 570659 19385438 ~ 19388378 (+) True XLOC_004666
TCONS_00010732 lncRNA upstream 687881 19267759 ~ 19271156 (+) True XLOC_004660
TCONS_00009224 lncRNA upstream 818386 19139343 ~ 19140651 (+) True XLOC_004655
TCONS_00010915 lncRNA upstream 1091062 18861278 ~ 18867975 (+) True XLOC_004648
TCONS_00010916 lncRNA downstream 289053 20263585 ~ 20265465 (+) True XLOC_004675
TCONS_00009263 lncRNA downstream 369357 20343889 ~ 20346635 (+) False XLOC_004677
TCONS_00010917 lncRNA downstream 369367 20343899 ~ 20346635 (+) False XLOC_004677
TCONS_00010919 lncRNA downstream 517087 20491619 ~ 20500564 (+) False XLOC_004679
TCONS_00010918 lncRNA downstream 517087 20491619 ~ 20500564 (+) False XLOC_004679
TCONS_00009248 mRNA upstream 26414 19866865 ~ 19932623 (+) False XLOC_004671
TCONS_00009247 mRNA upstream 299781 19408373 ~ 19659256 (+) True XLOC_004669
TCONS_00009246 mRNA upstream 556087 19401854 ~ 19402950 (+) True XLOC_004668
TCONS_00009242 mRNA upstream 565069 19384615 ~ 19393968 (+) False XLOC_004666
TCONS_00009241 mRNA upstream 576642 19362547 ~ 19382395 (+) True XLOC_004665
TCONS_00009253 mRNA downstream 1868 19976400 ~ 20045101 (+) True XLOC_004673
TCONS_00009254 mRNA downstream 147724 20122256 ~ 20149558 (+) False XLOC_004674
TCONS_00009255 mRNA downstream 147939 20122471 ~ 20147764 (+) False XLOC_004674
TCONS_00009256 mRNA downstream 147948 20122480 ~ 20125574 (+) False XLOC_004674
TCONS_00009257 mRNA downstream 148179 20122711 ~ 20147219 (+) False XLOC_004674
TCONS_00009249 other upstream 54622 19866998 ~ 19904415 (+) False XLOC_004671
TCONS_00009250 other upstream 62110 19877842 ~ 19896927 (+) True XLOC_004671
TCONS_00009245 other upstream 570764 19388143 ~ 19388273 (+) True XLOC_004667
TCONS_00009243 other upstream 573482 19385426 ~ 19385555 (+) False XLOC_004666
TCONS_00009203 other upstream 1259415 18681423 ~ 18699622 (+) False XLOC_004646
TCONS_00009270 other downstream 524451 20498983 ~ 20499080 (+) True XLOC_004679
TCONS_00009286 other downstream 716826 20691358 ~ 20692013 (+) False XLOC_004688
TCONS_00009295 other downstream 1462814 21437346 ~ 21437458 (+) True XLOC_004691
TCONS_00009299 other downstream 1819470 21794002 ~ 21794116 (+) True XLOC_004694
TCONS_00009304 other downstream 2469097 22443629 ~ 22444772 (+) True XLOC_004697

Expression Profile

//

Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000063_01890725_01899483.mRNA True 2961 mRNA 0.46 10 CI01000063 1890392 ~ 1899546 (-)