Sequence
atgc intronic sequence ATGC exonic sequencegtaggtgttctatcacacaaatttgatctcctgtattttttattcacaggcagtagtagttgtgaacatttactttttttattctttgattgaaagcttatgttcccatgacccagGTGTATACGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGAATGGC
Basic information
species | Glycine max |
transcript | GLYMA06G07050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G07050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G25320.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggtgttctatcacacaaatttgatctcctgtattttttattcacaggcagtagtag-ttgtgaacatttactttttttattctttgattgaaagcttatgttcccatgacccagGTGTATACGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGAATGGC
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----------------------gtgagtggttagattttttccatatctctaatcctggattattaatgtttatgatctccaattgcttaatgtgtgcct-----cgtataatgcagGTGTATATGAGTCCTTTGACACCATATGCATATATTTAGAGAGTGATCAATCTGCGGGTACAGATGTGGACAATAATTTCTGGGTTAAGTACAAGATGGG
upper sequence: GLYMA06G07050.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 2
gtaggt-gttctatcacacaaatttgatctcctgtattttttattcacaggcagtagtagttgtgaacatttactttttttattctttgattgaaagcttatgttcccatgacccagGTGTATACGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGAATGGC
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gtgagttgttgtttcttttaattttgactttctttgtt------------gaaattgtggttacaattatttacctttct--tttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaacatttactttttttattctttgattgaaagcttatgttcccatgacccagGTGTATACGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGAATGGC
ctttgat putative branch site (score: 5)
tgttccc putative PPT
atttactttttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtgttctatcacacaaatttgatctcctgtattttttattcacaggcagtagtagttgtgaacatttactttttttattctttgattgaaagcttatgttcccatgacccagGTGTATACGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGAATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT