Sequence
atgc intronic sequence ATGC exonic sequence...caaccattcaccgtgttagttttcactgtggataactgggccgctaattttaatacttatcaattatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
Basic information
species | Glycine max |
transcript | GLYMA17G04580.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 11
caaccattcaccgtgttagttttcactgtg--gataactgggccgctaattttaatacttatcaatta-tgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
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---catttctaagcatgtgtttctgatgcactagcagctagcttgaaagaaaacattcttttctgcaactgacttgtgaaccttttcttaattgggtatttagGTGGATTGTACTCTGGTGGCAGTGCTCAGATGGTTGAGAAGTCACTAGACATCCATGGAGATGAAATATTATATGTGGGGGATCATATTTACACAGATGT
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 10
--caaccattcaccgtgttagttttcactgtggataactgggccgctaattttaatacttatcaattatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
| || | | || | | ||| | || | | | | || | | | | || | || | | | | | ||||||| || || || || || ||||| || |||||||| || || ||||| |||||||| ||||| ||||| |||||||| |||||||||||||| |||||
atcctacaacctcagtttctttcttcgatatgctcttgtctattatccactgccagttttgtgactgac--tcgctatcccttttatgaaatgggtatttagGTGGCTTATATTCTGGTGGTAGTGCTCAGATGGTTGAGAAATCACTAGACATTCATGGGGATGAGATATTATATGTTGGGGACCATATTTACACAGATGT
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 11
caaccattcaccgtgttagttttcactgtggataactgggccgctaattttaatacttatcaa-ttatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
||| | | |||| |||| | | || | ||| |||| | || || || | || | || ||| || |||| |||||||||||||| |||||||| |||||| | || | ||| || | ||||||||||||| || ||||||||||| ||||| || |||||||||||
--gtaatttctcatt---gtttctactga----atttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 11
---caaccattcaccgtgttagttttcactgtggataactgggccgctaattttaatacttatcaattatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
|| | | ||| | | || || || | || | | || | |||| ||| | | | | | | || || ||| || || |||||||| || ||||| || ||| ||||||||||||| | || ||||||||||| || |||||||| || ||||| ||| | || |||||
tgttttccggagatcac-ttaatctgcaaaatgttaaataaaattgtaaactgtcatggt--tcaactattttgtgtattcatccttcttatattttttgcagGGGGCTTATACTCAGGAGGGAGTGCTCAGATGATTGAAAATTCCCTTAAAATCCATGGAGATGAGATTTTGTATGTCGGTGACCACATTCATACAGATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttaatacttatcaattatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
atcttac putative branch site (score: 3)
cactttatcttaccct CT-rich tract
taatacttatcaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaccattcaccgtgttagttttcactgtggataactgggccgctaattttaatacttatcaattatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
caaccat
- - - - - ccgtgtt
- - - - - - - - - - - - actgtgg
- - - - - - - - - - - - - - - - - - - -gccgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggca