Sequence
atgc intronic sequence ATGC exonic sequencegtatgtattatatcttttgatttgtaattatttgatcatacacctttttctcttagctcttatttttttaacctgaattttgcatttcttgcaatgacagAGACCTGCAGGGAAATAAACTAACTGGTCAAATTCCAGATGAAATTGGAAACTGTGCTGAACTTATTTATCT
Basic information
species | Glycine max |
transcript | GLYMA09G27950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G27950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G07180.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtatgtattatatcttttgatttgtaattatttgatcatacacctttttctcttagctcttatttttttaacctgaattttgcatttcttgcaatgacagAGACCTGCAGGGAAATAAACTAACTGGTCAAATTCCAGATGAAATTGGAAACTGTGCTGAACTTATTTATCT
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gttcgtttctcttctctctttt-acttgta--tgtttgagaagaaacat----------ggtgttaaatcctta---tgaagctctggtctttcttaattacagAGACTTGCAAGGAAATAAATTGGGTGGTCAAATTCCAGATGAGATTGGAAACTGTGTTTCTCTTGCTTATGT
upper sequence: GLYMA09G27950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G62230.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtattatatcttttgatttgtaattatttgatcatacaccttttt---ctcttagctcttatttttttaacctgaattttgcatttcttgcaatgacagAGACCTGCAGGGAAATAAACTAACTGGTCAAATTCCAGATGAAATTGGAAACTGTGCTGAACTTATTTATCT
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----gtaatggttttttttccctttctttctctgttgatttgcatgtttgaactttgaaatgttgtagcttttgttcata---aaggctttttccaattgcagAGACTTGCAAGGTAATAAACTAGCAGGTCAAATTCCAGATGAGATTGGAAACTGTGCTTCTCTTGTTTATCT
upper sequence: GLYMA09G27950.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtattatatcttttgatttgtaattatttgatcatacacctttttctcttagctcttatttttttaacctgaattttgcatttcttgcaatgacagAGACCTGCAGGGAAATAAACTAACTGGTCAAATTCCAGATGAAATTGGAAACTGTGCTGAACTTATTTATCT
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gtatttctttcacttgattgctttcaa--gcttatttccaacccattttctcacgacacatgattaagtctgttgttttttgtttgaatt----tggcagAGACCTGCAGGGGAATAGATTAACTGGTCAACTCCCAGATGAGATTGGCAACTGTGTTTCTCTTTCAACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctcttagctcttatttttttaacctgaattttgcatttcttgcaatgacagAGACCTGCAGGGAAATAAACTAACTGGTCAAATTCCAGATGAAATTGGAAACTGTGCTGAACTTATTTATCT
ttttaac putative branch site (score: 2)
tttcttgc putative PPT
ttatttttttaacctg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtattatatcttttgatttgtaattatttgatcatacacctttttctcttagctcttatttttttaacctgaattttgcatttcttgcaatgacagAGACCTGCAGGGAAATAAACTAACTGGTCAAATTCCAGATGAAATTGGAAACTGTGCTGAACTTATTTATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG