Sequence
atgc intronic sequence ATGC exonic sequencegtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 7
-gtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
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gttcttatgatccgagtatcattatttattctaaggca--ttacat----cgagtctgaaggatttccaatggca---cagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTA
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 6
-----------------------gtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatc-atttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
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atatttaatttttgatcatacgaatttcaagccctttag-ttaacttgttcttaatgattgatctctttatctattgcctat---tttgtcttttttatttcagAATATCGTGTTGTCTGGAGGTTCAACAATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTTAAGAAAATAGTGGACGCCCGTGCCCTTTCATCTG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 6
-----------------------gtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
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atatttaatttctgatcatatgaatttcaagccctttagtttacatgttcttaatgattgaattcttctcctctttcctattttgtctttt---ttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTACTTTTATCTG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 6
-----------------------gtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
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atatttaatttctgatcatataaatttcaagccctttagtttacatgttcttaatgattgaattcttcacctctttcctattttgtctttt---ttacttcagAATGTAGTGTTGTCTGGAGGTTCAACCATGTTCAAGGATTTTCACAGGAGGTTGCAACGTGATCTAAAAAAAATAGTGGATGCTCGTGTCCTTTTATCTGMapped 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|125249718|gb|EL263803.1|EL263803EST: ACACGAAGAGCTTTATATAAG AATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGG
genomic: ACACGAAGAGCTTTATATAAGgtttgaaacg ... atcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
tactgat putative branch site (score: 2)
tcatttc putative PPT
taagataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGGTTACAAAGGGACCTCAAGAAGATTGTTGATGCTCGTGTTCTTGCTAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG