Sequence
atgc intronic sequence ATGC exonic sequencegttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
Basic information
species | Glycine max |
transcript | GLYMA10G44540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g20150.1 (Oryza sativa), 3'ss of exon 5
---gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
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gtggtgatccctttctgcagttttgaac-----aatctcttcattggattactttact--tagtttgatcttttcatgt----------cgacagCAAGAAATCAAGCATACTATACAAAACAAACTTCATCGTAATGCTGGACCTGAGGATCTTATTGCTACAGAAGTCATGCTTGCTAGGATTACTAAGACCC------------
upper sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
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---------gtaataactcttttctcctgttttgtcatt--agatcagtttttttaatgg--tatccatataacatatc---tatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACC-GAGACCC-----------
upper sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctc-cagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
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gttgtattaattataatgagtggtgaattggttcttaatgttttcaaa---taaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC------------
upper sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25586 (Selaginella moellendorffii), 3'ss of exon 4
gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
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------------------------------gtatttgtgaacattcgacttcgtt--ttggctaatgacgtggtgtatttgtaaaagt--agCAAGAGATAAAGCATACAATCCAGAACAAACTGCACAGAAATGCTGGTCCAGAAGATTTGGTTGCGACAGAAGCATTATTAGCTCGTGTGACCAAAACAC------------
upper sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ22307 (Selaginella moellendorffii), 3'ss of exon 4
gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
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------------------------------gtatttgtgaacattcaacttcgtt--ttgactaatgacgtggtgtatttgtaaaagt--agCAAGAGATAAAGCATACAATCCAGAACAAACTGCACAGAAATGCTGGTCCGGAAGATTTGGTTGCGACAGAAGCATTATTAGCTCGTGTGACCAAGACAC------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
tgttaat putative branch site (score: 3)
aattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG