Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
Basic information
species | Glycine max |
transcript | GLYMA01G42960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
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---------gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatc--cttcattagttggagaattagatgaacatggatttta------------attttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttctta-aacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT------------------------
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gtaagtcagatcaccttacattgttggtttggttatcctaggctatcattcatta-ctcacccccaatgaatctcatctgttttagtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCATGTGAAATTGGCAGATTTTGGAATGGCAAAGCATGTAAGAGTATTCACATGCATTTTT
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
|||||| | || || | | || | | | ||| | | | || | | ||| | | | | || || | || || | | || ||||| |||| |||||| ||| |||||||||| ||||| | || ||||||||||||||||| ||||||||||||
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
tattaat putative branch site (score: 2)
ttttactc putative PPT
ttcttaaacttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG