Sequence
atgc intronic sequence ATGC exonic sequence...agctgcgtgatttgaatgcaactttatatccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55020.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
agctgcgtgatttgaatgcaactttatat--ccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacga-atatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
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---gactccattttgctgtcattttttttgacatataatctagcaaatacatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
-----agctgcgtgatttgaatgcaactttatatccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
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catgtcaatgcctttttatactgctatattatat--ttcgactagcacaatgatgaatttttgtactgcaacatcttacaatcatacatattata-ttgac--agGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
-----agctgcgtgatttgaatgcaactttatatccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
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catgtcaatgcctttttatactgctatattatat--ttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacatattata-ttggc--agGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCCMapped 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|124764996|gb|EH855126.1|EH855126EST: GCTCAAGTCTTGCAG GAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCA
genomic: GCTCAAGTCTTGCAGgtaaaaagtt ... actggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
tgataac putative branch site (score: 2)
aatatgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctgcgtgatttgaatgcaactttatatccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacgaatatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCC
- - - - gatttga
- - - - - - - - - - - - - - - cttttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaat