Sequence
atgc intronic sequence ATGC exonic sequence...ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
Basic information
species | Glycine max |
transcript | GLYMA04G26840.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 6
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
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------------------gtaattatgca--aaatttacagatataccacatctcatgtttgatcctttgttaataaatctgataccctt---ttcttagGTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGA
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
-------------------------------------ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttg-attatgatgttcacttt--tatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
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gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaaga---tgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
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---------gtaattatactgattgcaaaacgcatagatacaactttgtgtcactatactcgg----cgcttctgataat-----------aatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttt----tatgaaa--tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
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------------------------gtaagttttgctactttccttgtatgttt--ataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 6
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttt----tatgaaa--tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA--------------
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------------------------gtaagttttgctactttccttgtatgttt--ataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCAGTATCCTTATAACT
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttat----gaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
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-tatgtcatcaactagtatacagcttattttagaatactttccttgata--ttgga-actgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctagtttgaatatttaagctttgattatgatgttcacttttatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
ctttgat putative branch site (score: 5)
ttttatgaaatgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt