Sequence
atgc intronic sequence ATGC exonic sequence...tgtgttcaagatagaaagatgctttggatctttatccttctcttgaaacagcatggctaatcttaattttattgctctcttttgttcttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23100.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------tgtgttcaagatagaaagatgctttggatctt---tatccttctcttgaaacagcatggctaatcttaattttattgctctcttttgttc--ttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
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gttagtatatataatttcataccattcgaccctcttcccccacccagaacactggcaatttgattgaagacctcattttggccaaagatattttacacatgaaatgaaggtttccatgttactgaaatt-ctgattatagtttgtttctttgatgcagGTTTGAGCGATATGTGGACTATGCATTAGATGTCCCGATGTATTTTGTCTATCGAAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------tgtgttcaagatagaaagatgc--tttgg--atctttatccttctcttgaaacagcatggctaatcttaattttattgctctcttttgttc--ttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
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gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaaacctcattttggccaaagatattttatacatgaaatga-aggtttccatgtaactgaaattctgattatagttcgtttctttgatgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 9
--tgtgttcaagatagaaagatgctttggatctttatccttctcttgaaacagcatggctaatcttaattttattgctctcttttgttcttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
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ccctttcttttattttttttacaattttatcaattatatttca--tgcaatgacttggtttttttttttttcactttttttcttctaactttctgattgcagGTTTCAGCAGTATGTTGATTATGCACTTGATGTTCCTATGTATTTTGTCTATCGGAAACACAGATATATCGACTGTACTGGAAAGACCTTCAGG
upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 9
tgtgttcaagatagaaagatgctttggatctttatc-----cttctcttgaaacagcatggctaatcttaattttattgctctcttttgttcttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
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tgaattcctttcttt----ttttttacaattttatcaatgatatttcatgcaatgacttggttaattgtttttcactttttttcttctaactttctg-attgcagGTTTGAGCAATATGTTGATTATGCTCTTGATGTTCCTATGTATTTTGTCTATCGGAAAAACAGATATATCGACTGCACTGGAAAGACCTTCAGGMapped 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|47830326|gb|CK120010.1|CK120010EST: GACAAGGACCGCACAGGAATGCTACCATTTGTTTTCGATGACTCTTTTGG GTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTA
genomic: GACAAGGACCGCACAGGAATGCTACCATTTGTTTTCGATGACTCTTTTGGgtgagtatcg ... tctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacagcatggctaatcttaattttattgctctcttttgttcttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
tcttaat putative branch site (score: 3)
ttttattgctctcttt CT-rich tract
taatcttaattttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgttcaagatagaaagatgctttggatctttatccttctcttgaaacagcatggctaatcttaattttattgctctcttttgttcttatctggtatagGTTTGAGCAGTATGTTGACTACGCACTCGATGTCCCTATGTACTTTGCCTACAGAAAGAACAAATACATCGACTGTACTGGAATGACATTTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC