Sequence
atgc intronic sequence ATGC exonic sequence...tcttatgttgtgtgattcttgtaaagtctaaatatgaaaaatctgtctctgatttatagaagatttccctatttgactttggttatgtatacctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
Basic information
species | Glycine max |
transcript | GLYMA08G18920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------------------tcttatg------ttgtgtgattcttgtaaagtctaaatatga-aaaatctgtctctgatttatagaagatttccctatttgactttg-gttatgtat--acctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
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gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
upper sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 5
tcttatgttgtgtgattcttgtaaagtctaaatatgaaaaatctgtctctgatttatagaagatttccctatttgactttggttatgtata---cctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
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--ctttattctgttgttcttctaattgtctgaca-gttctttccgtttatttcctggacgtcatgcttttatataatctgtcttttttttggcccttatgcagCTAGAAGGAGAGGCAACTGCTAGAGCTATTCGGTTGGCCAGTTTTGTTAACACGCCTCTCTATGTAGTTCATGTGATGAGCATTGATGCGATGGAAGAAA
upper sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ32862 (Selaginella moellendorffii), 3'ss of exon 4
tcttatgttgtgtgattcttgtaaagtctaaatatgaaaaatctgtctctgatttatagaagatttccctatttg-actttggttatgtatacctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
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--------------------------------------------gtaagcaaaacttttaatattgctttcttcatacttttcttttacatgc----gaagCTGGAAGGAGAAGCCACAGCACGAGCCATCAGACTTGCAAAGTTTGTAAACACGCCTCTGTATGTGGTTCACGTAATGAGCATAGATGCACTGGAAGAGA
upper sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14600 (Selaginella moellendorffii), 3'ss of exon 4
tcttatgttgtgtgattcttgtaaagtctaaatatgaaaaatctgtctctgatttatagaagatttccctatttg-actttggttatgtatacctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
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--------------------------------------------gtaagcaaaacttttaatatttctttcttcatacttttcttttacatgc----gaagCTGGAAGGAGAAGCCACAGCACGAGCCATCAGACTTGCAAAGTTTGTAAACACGCCTCTGTATGTGGTTCACGTAATGAGCATAGATGCACTGGAAGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctgatttatagaagatttccctatttgactttggttatgtatacctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
atttgac putative branch site (score: 4)
atttatagaagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttatgttgtgtgattcttgtaaagtctaaatatgaaaaatctgtctctgatttatagaagatttccctatttgactttggttatgtatacctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - tgtgtga
- - - - - - - - - - - - - - - - - -gaaaaat
- - - - - - - - - - - - - - - - - - - - - ctgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactttg