Sequence
atgc intronic sequence ATGC exonic sequence...ctagtagcaaaatactaaaacaagtgacagaaaaacttttgattgctttatctaaccttttggcgttgtctgaataccaactatctgttatatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
Basic information
species | Glycine max |
transcript | GLYMA11G06720.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
ctagtagcaaaatactaaaacaag-tgacagaaaaacttttgattgctttatctaaccttttggcgttgtctgaataccaactatctgttatatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
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---gtat--atatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtat---agGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
ctagtagcaaaatactaaa--acaagtgacagaaaaacttttgattgctttatctaaccttttggcgttgtctgaataccaactatctgttatatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
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gtatatatacaggaccaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacc--cttttttttgtata-----gGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
-----ctagtagca--aaatactaaaacaagtgacagaaaaact-tttgattgctt--tatctaaccttttggcgttgtctgaataccaactatctg---ttatatattga---agGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
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gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctca-tatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
-----ctagtagca--aaatactaaaacaagtgacagaaaaactt--ttgattgcttta--tctaaccttttggcgttgtctgaataccaactatctgttatatattga---agGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
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gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
ctagtagcaaaatactaa-aacaagtgacagaaaaactt--ttgattgctttatctaaccttttggcgttgtctgaataccaact-atctgttatat------attgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
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----------aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttatctaaccttttggcgttgtctgaataccaactatctgttatatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
atctaac putative branch site (score: 2)
tatctgttatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagtagcaaaatactaaaacaagtgacagaaaaacttttgattgctttatctaaccttttggcgttgtctgaataccaactatctgttatatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - aaaacaa
- - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacta