Sequence
atgc intronic sequence ATGC exonic sequence...atctgttggatattcgtaggtagttatatatatattatatattaacgaaaactcttctctggtattcaggctactgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18230.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 3
---------------------------------atctgttggatattcgtaggtagttatatatatattatatattaacgaaaactcttctctggta--ttcaggct-actgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
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gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 3
-----------------------------atctgttggatattcgtaggtag-ttatatatatattatatattaacgaaaactcttctctggtattcaggctactgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
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gtgagtctttgacacagggaaatatgcttttttattttatttttatttttggcttttctaggtgtattatgattatgcttcctttt-taggggatgaagagtatcttattctcaatgctttgtg--acagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 3
--------------------------------atctgttggatattcgtaggtagttatatatatattatatattaacgaaaactcttctctggtattcaggct-actgatttgtcagcttca-tgttttat---agGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
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gtgagtctttgactcagggaaatacgttttttttttttcttatattt-tgggcttttctaggtgtattatgattatgcacttatgcttcctctttag--gggctgaagaatctcttattctcaatgttttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
upper sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 3
--atctgttggatattcgtaggtagttatatatatattatatattaa--cgaaaactcttctctggtattcaggctactgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
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gcaccggtttaatata---aagtactctaattta-gtcatgttttaaattttaaaatctaaccttttaatcagattgtttatcatgtaattctttttttgatagGACCCAAAGGAGAAGGCTAAATCAGAGACAAGGGACTGGTTGAACACTGTGMapped 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|116424325|gb|EG466917.1|EG466917EST: CCAAGACAAAAGCCTTCTCCAAGGAAGGACTGGGTCAGCAACCTAAAACT GACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CCAAGACAAAAGCCTTCTCCAAGGAAGGACTGGGTCAGCAACCTAAAACTgtaagaattt ... tgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
EST:
gi|164168634|gb|ES046895.1|ES046895EST: CCAAGACAAAAGCCTTCTCCAAGGAAGGACTGGGTCAGCAACCTAAAACT GACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CCAAGACAAAAGCCTTCTCCAAGGAAGGACTGGGTCAGCAACCTAAAACTgtaagaattt ... tgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaaaactcttctctggtattcaggctactgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
tactgat putative branch site (score: 2)
atgttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctgttggatattcgtaggtagttatatatatattatatattaacgaaaactcttctctggtattcaggctactgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - -aacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgt