Sequence
atgc intronic sequence ATGC exonic sequencegttctactacctgttttacctctctctttaatgtttatacattgttgttatctttatacaagataatttatggctgaacaacaatgtcaagatgatcttacttgggggttattcttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG
Basic information
species | Glycine max |
transcript | GLYMA09G39480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39480.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 3
gttctactacctgttttacctctctctttaatgtttatacattgttgttatctttatacaagataatttatggctgaacaacaatgtcaagatgatcttacttgggggttattct--tgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG
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------------------------------------------gtttgtttgaattagaagtaaatattttcatttccataccc-cgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG
upper sequence: GLYMA09G39480.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G61415.2 (Arabidopsis thaliana), 3'ss of exon 3
gttctactacctgttttacctctctctttaatgtttatacattgttgttatctttatacaagataatttatggctgaacaacaatgtcaagatgatcttacttgggggttattcttg---tatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG
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--------------------------------gtttacttgaggttattaaatttg----aaacaattaatgacatgtcgattatcctatgcctttttttcatagagctctttgttactttttagGAACGTAAAGTTTATGATGAAAAATTCATCCGGATGGATACAAAGAGGCTCTGTGAGTTGACCTCAGCCGCTGACAGTTTGCAGTTGAAGCCGTTGGTTG
upper sequence: GLYMA09G39480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02450.t01 (Vitis vinifera), 3'ss of exon 2
gttctactacctgttttacctctctctttaatgtttatacattgttgttatctttatacaagataatttatggctgaacaacaatgtcaagatgatcttacttgggggttattcttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG
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-gtttgc-acatatctaacttatcattttc-tttttctgattagatgttctttt-------gctagttt------gaatagcaaagctatgtttgacct-tttggccattttttgggcatagGAGCGGAAATCTTTTGATGAGAAGTTCATTAGAATGGATACAAAGAGGCTATGTGAGTTGACATCTGCTGCTGACAGCCTCCAATTGAAGCCTTTGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatggctgaacaacaatgtcaagatgatcttacttgggggttattcttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG
atcttac putative branch site (score: 3)
ttattctt putative PPT
ttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctactacctgttttacctctctctttaatgtttatacattgttgttatctttatacaagataatttatggctgaacaacaatgtcaagatgatcttacttgggggttattcttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTAAAGCCATTGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG