Sequence
atgc intronic sequence ATGC exonic sequence...gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaaatagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
Basic information
species | Glycine max |
transcript | GLYMA15G21780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G36060.2 (Arabidopsis thaliana), 3'ss of exon 3
gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaa-atagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
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------------------------gtaagagt---gtgaattttttgagatttgttgcttttgaattaggtgactgaaat-gtgaatttgcatatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACAATGGAGGACATACTGACTCAATTGAAGAAGGAGATGGCTGCATCGCATA
upper sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 3
gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaaatagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
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--------gtacgtataaactcaccaccgcccttcctttctctgttttgtttctt---tggatg-ctctgtaatt---tttttatgcgtatgtgta-tagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACAATGGAGGATATACTGGTACAGTTGAAGAAGGAAATGTCTACGTCGCATA
upper sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 3
gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaa-atagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
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----------------------gtggtaagagt--gtgaattttttgagatttgttgcttttgaattaggtgactgaaat-gtgaatttgcatatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACAATGGAGGACATACTGACTCAATTGAAGAAGGAGATGGCTGCATCGCATA
upper sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 3
-gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaaa--tagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
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aaatctttgtcatattcctgaat-tccaaatttatggatcattaaaaggtctcagta-cgagttgcctt-gcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggcttaataactaattatctttgtgacaagatttatagacttgaatgaaatagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
ttaataactaattatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaaatagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacaag