Sequence
atgc intronic sequence ATGC exonic sequence...atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
Basic information
species | Glycine max |
transcript | GLYMA08G04110.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G04110.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 4
atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtg----tgatata---tattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
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-------ttagctacacatcatgtaaaagaagatccatttttacagacaaagatacaaaaacgagatcctgacatggctaacctctttctctcttttttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG
upper sequence: GLYMA08G04110.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------atgctctttgtttatat-agcatt--acatagaa-gagaagagatgactgagaatatgactgt-agtgtgtgatata---tattttgattttttttttac-----ttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
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gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
upper sequence: GLYMA08G04110.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
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gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggtt-gattgatccctt-ttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
upper sequence: GLYMA08G04110.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 4
-------atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
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atggttcccccccccctttttttttttttttttttcagaaataaagaagac-gtgaatatgactttggagggt----tgtggtgtggtttttttct--cttttgcagACTGACACAGCTTCTGTCTTGTTAGAAGCTATTGGTTATATCAGATTCCTCCAGAGTCAAATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
ttttgat putative branch site (score: 4)
ttttgatttttttttt CT-rich tract
tgtgtgatatatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - gcattac
- - - - - - - - - - - - - - gaagagaa
- - - - - - - - - - - - - - - - - - - -atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg