Sequence
atgc intronic sequence ATGC exonic sequence...tgtagaccaaaaatgtagtagtacatgtttatgtttggattatattatggtctcaatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
Basic information
species | Glycine max |
transcript | GLYMA15G41740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G41740.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------tgtagaccaaaaatg--tagtagtacatgttta--tgtttggattat-attatggtctcaatgatcttttgattaatcatctttttct--------cttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
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gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgtttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
upper sequence: GLYMA15G41740.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g07770.1 (Oryza sativa), 3'ss of exon 1
-tgtagaccaaaaatgtagtagtacatgtt-tatgtttggattatattatggtctcaatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
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gtacgcatcatcaatctctcaatcaattctctccaaaaaaatcgaaacaagaattaatctcttctttcttacgatgaattgatgatcgtcttgtcgtcgcagAGGCGACGCCCAAGACGATCATGAGGGTGATGGGAGTGAAGGGCCTCACCCTCTACCACCTCAAGAGCCATCTCCAG
upper sequence: GLYMA15G41740.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G081671_T01 (Zea mays), 3'ss of exon 1
--------------------------tgtagaccaaaaatgtagtagtacatgtttatgtttggattatattatggtctcaatgatctt--ttgattaatcatctttttct---cttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
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gtacgtgatacatagagatgcatgctttcagttacgttacgtgttgctacttgccgctgtg-gaattttatt-tgata-cgttaattttggttgatttg-catccttccctaaattcttcgccgtacgtagAGGCAACGCCCAAGACCATCATGAGGGTTATGGGAGTCAAGGGCCTCACCCTCTACCACCTCAAGAGTCACCTTCAG
upper sequence: GLYMA15G41740.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
tgtagaccaaaaatgtagtagtacatgtttatgtttggattatattatggtctcaatgatcttttgattaatcatctttttctcttttttggattt--gcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
||| | | || || | || | | | ||| | | || | | | | ||| ||| ||| |||| | |||||||| ||||| || |||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||||
-gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgtttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggtctcaatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
gattaat putative branch site (score: 3)
tctttttctctttttt putative PPT
attaatcatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtagaccaaaaatgtagtagtacatgtttatgtttggattatattatggtctcaatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG
- - -accaaaa
- - - - - - - - - - -tacatgt
- - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - -ctcaatg