Sequence
atgc intronic sequence ATGC exonic sequence...gatcttgcttttagatgcatctgtttttgtagtacttttatactgctttttctttctttttataagttggtggcatctcagcggggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 4
gatcttgcttttagatgcatc--tgtttttgtagtacttttatactgctttttctttctttttataagttggtggcatctcagcggggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
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--ctacatatttaagcacaccaatattttcttattcgtctgttagttataaccgtttcttgtttgtatatagtgaatttacaatgctatcttgttgtttcagGGGAAGAGAGGTATTGAGAAACAGCCTTTCCAGCTTCCTGACTTCATTGCTGCAACTGGAATAGAAAAGATAAGACAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 5
-gatcttgcttttagatgcatctgtttttgtagtacttttat--actgctttttctttctttttataagttggtggcatctcagcggggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
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tcgtcttatcttcaattttttatgattg-atattacttatcccaattacatagtgtatgtccacataaagtacttatatctcatcaa--tttttttttggcagGGTAAACGAGGTATAGAGAAACCAGCCTTTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 5
gatcttgcttttagatgcatctgtttttgtagtactt--ttatactgctttttctttctttttataagttggtggcatctcagcggg----gtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
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-----tatcttcaattttttatgattg-atattacttagcccaattacatagtgtatgtccacataaagtacttatatctcatcaattattatcttttcttggcagGGTAAACGAGGTATAGAGAAACCACCCTTTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 2
------gatcttgcttttagatgcatctgtttttgtagtactt--ttatactgctttttctttctttttat--aagttggtggcatctcagcgg-----ggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
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atgcttggggtgaattcctcttgtcttcaatgttttagtgcttggccacagaacttcatagtcatgtacatgtaatttacttatatctcatcaaatgtagTTATGGTTTTTGCTGGGGAAAAGAGGTATAGAGAAACCACCCTTTCAGCTTCCTGATTTCATTGCTGCCACAGGAATTGAGAAAATCAGACAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 5
gatcttgcttttagatgcatctgtttttgtagtactt--ttatactgctttttctttcttttta--taagttggtggcatctcagcggggttt-----catttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
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---------cttcaatgttttaaaatctatagtgcttggtcacagaacttcatagtcatgcacatgtaatttacttatatctcgtaaaaaattgttattgtttttgcagGGTAAAAGAGGTATAGAGAAACTTCCCTTTCAGCTTCCTGATTTCATTGCTGCCACAGGAATTGAGAAAATCAGACAG
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 5
gatcttgcttttagatgcatctgtttttgtagt--acttttatactgctttttctttctttttataagttggtggcatctcagcggggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
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--tacacatgtcgcagacatcacaccacagaatttgtcctggtggaccattttgattcagattttgattcgggacttgttctgatggtgattttgttttcagGGGAAGCGTGGTATAGAGAAGCAGCCCTTTCAGCTTCCCGATTTTATTGCAGCAACTGGTATTGAAAAAATAAGACAGMapped 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|164176367|gb|ES041031.1|ES041031EST: ATACAGTTCCTGTTCCAAGACATTGGTCGCAGAAGAGAAAATATTTGCAG GGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCC
genomic: ATACAGTTCCTGTTCCAAGACATTGGTCGCAGAAGAGAAAATATTTGCAGgtttgtgata ... atttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttctttctttttataagttggtggcatctcagcggggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
tttcattttt CT-rich tract
tttctttttataagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatcttgcttttagatgcatctgtttttgtagtacttttatactgctttttctttctttttataagttggtggcatctcagcggggtttcatttttgcagGGAAAGCGTGGGATAGAGAAGCAGCCATTTCATCTTCCTGATTTCATTGCTGCAACCGGAATTGAGAAGATTAGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC