Sequence
atgc intronic sequence ATGC exonic sequencegttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
Basic information
species | Glycine max |
transcript | GLYMA08G28890.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
-------------gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatca-tcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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gtagcacattctggttgtcctggaagtta-atactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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-------------gtaccacttcctggttca--ctaggaattaaagcttcatgcagacattctagtactgtcattcctgaaacaaagtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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----------------------gttgatcaacgtctttaacatatgattgatacatcttccaga---gagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtct---tatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactttctcccagtggttgacttttataactttcttgtcttatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
ttataac putative branch site (score: 2)
tcatttt putative PPT
ttttataactttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG