Sequence
atgc intronic sequence ATGC exonic sequence...ttcggtgggtttttgtaactttgctacttatctcatagttgattaagagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01560.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 1
--ttcggtgggtttttgtaactttgctacttatctcatagttgattaagagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT
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ggtctgactaggagtaggag-ttcact-tttgttatccatgtgacatagactttctgttagcaaggacgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT
upper sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
ttcggtgggtttttgtaactttgctactt-atctcatag--ttgattaagagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT
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--aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgtt-ttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATTMapped 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|116443556|gb|EG486148.1|EG486148EST: TATGTTCCTCCTCTTCGTCCTATCGGCAGAGGCGCTTCTGGCATCGTCTG TGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGG
genomic: TATGTTCCTCCTCTTCGTCCTATCGGCAGAGGCGCTTCTGGCATCGTCTGgttagcatct ... tctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT
atctgat putative branch site (score: 4)
tttatct CT-rich tract
atcatttatttatctg TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcggtgggtttttgtaactttgctacttatctcatagttgattaagagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA