Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctatcgcaaacctctgcacatcttcttctttctgagggctttgaggtgtctcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G28690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
gtatgtctatcgcaaacctctgcacatcttcttctttctgagg-------gctttgaggtgtctcgtctaattaccatgtttttcttttttcatttgggt--tcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
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------gttgcgttaaatttggcccaactgtttcatttcagtataactctattctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
------gtatgt-ctatcgcaaacctctgcacatcttcttctttctgagggctttgaggtgtctcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
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aggattttatgtgctaaatttgaccagtgt-tgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaa---tagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
--gtatg-tctatcgcaaacctctgcacatc-ttcttctttctgagggctttgag-gtgtctcgtctaattaccatgttttt-cttttttcatttgggttcagGGACC-TTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
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tcctataatgcattgttc-tttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
upper sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
---gtatg-tctatcgcaaacctctgcacatc-ttcttctttctgagggctttgag-gtgtctcgtctaattaccatgttttt-cttttttcatttgggttcagGGACC-TTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
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ttcctataatgcattgttc-tttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
upper sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
---gtatgtctatcgcaaacctctgcacatcttcttctttctgagggctttgaggtgtc-tcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
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ataatgcatttgtt-ctttctgcttggcactatgctactaataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATAMapped 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|125263396|gb|EL277481.1|EL277481EST: ACGAGGAAGTTTGGAGAACCATCTTTTCAGAA GGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAG
genomic: ACGAGGAAGTTTGGAGAACCATCTTTTCAGAAgtatgtctat ... ttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctttgaggtgtctcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
gtctaat putative branch site (score: 3)
ccatgtttttcttttt putative PPT
tttttcttttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctatcgcaaacctctgcacatcttcttctttctgagggctttgaggtgtctcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC