Sequence
atgc intronic sequence ATGC exonic sequence...ttggtttgtgtgtattgtgcaatttggaatctatttgtatgcattttcttggtcttcctagtctctgacaaggtctgttctgttgtggtttgtttggcagTTGAATGTGGAATACCATTTCCCTGAAGATCCAAGATACTTTGACATCAACTGAAAATTCTAGTTTTCCTCCTAAAAAAAAAGCATGCTGCTTTTGCTGA
Basic information
species | Glycine max |
transcript | GLYMA16G05600.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05600.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G26890.3 (Arabidopsis thaliana), 3'ss of exon 6
-----------------ttggtttgtgtgt--------attgtgcaatttggaatctatttgtatgcatttt--cttggtcttcctagtctctgacaaggtctgttctgttgtggtttgtttggcagTTGAATGTGGAATACCATTTCCCTGAAGATCCAAGATACTTTGACATCAAC---TGAAAATTCTAGTTTTCCTCCTAAAAAAAAAGCATGCTGCTTTTGCTGA
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gtacgtatgagatttgtgtgttttgagtgttgaccatcgttttgcaaatcagcaaatagctaaaattagttgagttttatttttgtaaaag-tgataacaaaaatcatttatttgtctgtgttgcagTTGAATGTCGAGTACCATTACCCTGAAAACCCAAGATACTTCGACATCACCGAGTGAGAACT-TAACTTCATGGTTACACAAGCTCAATGATTTTCTTGTT--
upper sequence: GLYMA16G05600.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G41110.1 (Arabidopsis thaliana), 3'ss of exon 5
ttggtttgtgtgtattgtgcaatttgg--aatctatttgtatgcattt--tcttggtcttcctagtctctgacaaggtctgttc-tgttgtggtttgtttggcagTTGAATGTGGAATACCATTTCCCTGAAGATCCAAGATACTTTGACATCAACTGAAAATTCTAGTTTTCCTCCTAAAAAAAAAGCATGCTGCTTTTGCTGA
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-------gtatgt-tagaacaatttgagaaatttattcaaattcatttggtatagagctatttgaacgcaaacgcaaaacgctgatgttgcttttgaaattgcagTTGAATGTGGAGTATCATTACCCAGAAAATCCAAGATACTTCGACGTGTAA-------------------------------------------------
upper sequence: GLYMA16G05600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0068g01450.t01 (Vitis vinifera), 3'ss of exon 6
-ttggtttgtgtgtattgtgcaatttggaatctatttgtatgcattttcttggtc--ttcctagtctctgacaaggtctgttctgttgtggtttgtttggcagTTGAATGTGGAATACCATTTCCCTGAAGATCCAAGATACTTTGACATC---AACTGAAAATTCT-AGTTTTCCTCCTAAAAAAAAAGCATGCTGCTTTTGCTGA
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atttattgaactctctctctctctctcgc-tctctctctgtttgtttaatatatcagcactgaatgtttgtctaa-tgagaattgttgctggctgat-ggcagTTGAACGTGGAATACCATTACCCAGAAGATCCCAAATACTTTGACATCGGCAACTGAAATCTTTGAATTCATCTCCTCAGCTGTTCCCTTGCGGGCTTTG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttggtcttcctagtctctgacaaggtctgttctgttgtggtttgtttggcagTTGAATGTGGAATACCATTTCCCTGAAGATCCAAGATACTTTGACATCAACTGAAAATTCTAGTTTTCCTCCTAAAAAAAAAGCATGCTGCTTTTGCTGA
ctctgac putative branch site (score: 3)
tttgttt putative PPT
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggtttgtgtgtattgtgcaatttggaatctatttgtatgcattttcttggtcttcctagtctctgacaaggtctgttctgttgtggtttgtttggcagTTGAATGTGGAATACCATTTCCCTGAAGATCCAAGATACTTTGACATCAACTGAAAATTCTAGTTTTCCTCCTAAAAAAAAAGCATGCTGCTTTTGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - tgtgtgt
- - - - - - - -tgtgcaa
- - - - - - - - - - - - - - - - - - gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgtgg