Sequence
atgc intronic sequence ATGC exonic sequenceATGGTACCGTTTCTTTTTGAACAAGGATTATGGAAGCCTCTTCTCCTCTCTTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAGgtaggtggctttctagaattattggacctccctttttttttttgtggaagctaagggaaattggcaatgagattcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01960.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 5'ss of exon 5
ATGGTACCGTTTCTTTTTGAACAAGGATTATGGAAGCCTCTTCTCCTCTCTTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAGgtaggtggctttctagaattattggacctccctttttttttttgtg----gaagctaagggaaat-tggcaatgagattcag--------------------------------------
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TTGGTACCGTTTCTTTCTGAACAAGGAATATGGGAGTCTTTTCTCATCTTTAACCACTGGACTGTACCTGACCTTCAAGTTAACTTCAGTAGTTGAAAAGgta--ctacttttactagttactgtagctcacatacaaaattagtgctgtgaacctataaaatatatattttttccattccatgcatgcttattttctcattgttgactgtatgttccag
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G45010.1 (Glycine max), 5'ss of exon 5
ATGGTACCGTTTCTTTTTGAACAAGGATTATGGAAGCCTCTTCTCCTCTCTTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAGgtaggtggctttctagaattat-tggacctccctttttttttttgtggaagctaagggaaattggcaatgagattcag----------------------
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TTGGTATCGTTTCTTCCTGAACAAAGAATATGGAAGCCTCTTTTCATCACTGATGACAGGATTGTATCTAACATTTAAACTCACGTCTGTTGTTGAAAAGgtgtgttggtttttaaaaatacatgtagatactattttattttaatgtagcttgtgatcagtaacctccacaatttctctctcccccgttgaattatata
upper sequence: AT5G01960.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv08s0056g00440.t01 (Vitis vinifera), 5'ss of exon 5
ATGGTACCGTTTCTTTTTGAACAAGGATTATGGAAGCCTCTTCTCCTCTCTTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAGgtaggtggctttctaga----attatt----ggacctccctttttttttttgtggaagctaagggaaattggcaat----gagattcag--------------------------------------------------------------------------------------
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CTGGTATCGTTTTTTCTTGAACAAAGAATATGGGAGCCTATTTTCATCACTAATGACAGGGTTGTATTTAACTTTCAAGCTCACCTCTGTTGTTGAGAAGgtatgatgttctcttgatgtaaatattctatggattgatgcctctgtttctgcttttgctttgggtctttttttcttcctaatttttaatcctcctcatgaagattaacttcttggttctgtggatcttatgcttatttttttcctccctctctaccttgattggtgatgttcagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86080420|gb|DR376177.1|DR376177EST: TTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAG GTTCAATCCTTCTTTACGGCATTGAAGGCTTTGTCACGTAAAGAGGTGCAC
genomic: TTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAGgtaggtggct ... tgagattcagGTTCAATCCTTCTTTACGGCATTGAAGGCTTTGTCACGTAAAGAGGTGCAC
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGGTACCGTTTCTTTTTGAACAAGGATTATGGAAGCCTCTTCTCCTCTCTTATGACGGGATTGTATCTTACATTCAAGCTCACTTCAGTAGTTGAGAAGgtaggtggctttctagaattattggacctccctttttttttttgtggaagctaagggaaattggcaatgagattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA