Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctttatgtctctttaaaaattttctcatcaatttgtttcttgatcataacttctaatgtatttatgtgtataactatgtacaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
Basic information
species | Glycine max |
transcript | GLYMA20G00320.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
gtaagtctttatgtctctttaaaaattttctcatcaatttgtttcttgatcataacttctaatgtatttatgtgtataactatgt-acaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
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--------------gtaaggataaatctgaacttct-tttctcctttatttgggagttctatggcttttata-gtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
-----------------gtaagtctttatgtctctt----taaaaat-tttctcatcaatttgtttcttgatcataacttctaatgtatttatgtgta--taactatgtacaatt-------cagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
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gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatat-atgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtctttatgtctctttaaaaattttctcatcaatttgtttcttgatcataac-----ttctaatgtatttat-----gtgtataact---atgtacaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
|||||| ||||| | |||| ||| | | | | |||||| |||| | | | |||||||| ||||| |||| || ||| | |||| |||||||| || ||| ||||||| || |||||||||||| ||||||| | ||||| |||||||||||||| || || ||||||||| ||||||| |
gtaagtgtttatttttcttctaaacatatttt-ttaatttgcttctgaaatgtgccagtttctctaatgtttttattggtggtgtgcctcttatatgcttgttgtagACCAAAGCAGGACCAGTTCTGGTTGCCATCAATCCCTTTAAGGAAGTTCCGTTGTATGGAAATGATTATATTGATGCGTATAAGCGTAAATCAATTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttcttgatcataacttctaatgtatttatgtgtataactatgtacaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
ttctaatgtatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctttatgtctctttaaaaattttctcatcaatttgtttcttgatcataacttctaatgtatttatgtgtataactatgtacaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA