Sequence
atgc intronic sequence ATGC exonic sequencegtaagggtaaggagggtttggatggttcttgtttcaatagagttgcctagactgaacatatatctttttgttatattttcctctttaaaaaaatttgtccagctagagctaactgcttagtgcttatcgttcaattgattgcatttttgcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG
Basic information
species | Glycine max |
transcript | GLYMA11G07950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 6
gtaagggtaaggagggtttggatggttcttgtttcaatagagttgcctagactgaacatatatctttttgttatattttcctctttaaaaaaatttgtccagctagagctaactgcttagtgcttatcgttcaattgattgcatttttgcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG
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-------------gtgtggaaatgaattttctttcttt----cttcccag--tgaacctggatatagcaataagagtagcagctc-------atttgtttcttcag---------tctggtgatcattttgtttttgcttgtgtg---acagCTCAAAGACAGATTGGGGAAACTGCTATGAATGAAGCAAGCTCCAGATCTCATCAAATACTCAGGATG
upper sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 5
gtaagggtaaggagggtttggatggttcttgtttcaatagagttgcctagactgaacatatatctttttgttatattttcctctttaaaaaaatttgtccagctagagctaactgcttag--tgcttatcgttca---attgattgcattttt---gcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG--------------------------------
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------------------------------------------gtgc-taaaccaaagtttcgttttctt-ttccgttttcca-ttcgaagaaatgagatt-gcaagaagcatctcgttaggttacttctagtgcactaatcctctgtgtgcctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG
upper sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 5
gtaagggtaaggagggtttggatggttcttgtttcaatagagttgcctagactgaacatatatctttttgttatattttcctctttaaaaaaatttgtccagctagagctaactgcttagtgcttatcgttcaattgattgc--atttttgcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG
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------------------------------------------------------------------------gtaacaacattctgaaagca----gtccagcta----ttactgatgaacgcaaat-attaaatatcctgcgaattcttgcagCCCAGAGACAAATAGGGGAGACCGCACTTAATGAAACAAGCTCTAGATCTCATCAAATTCTCAGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccagctagagctaactgcttagtgcttatcgttcaattgattgcatttttgcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG
cattttt CT-rich tract
aattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggtaaggagggtttggatggttcttgtttcaatagagttgcctagactgaacatatatctttttgttatattttcctctttaaaaaaatttgtccagctagagctaactgcttagtgcttatcgttcaattgattgcatttttgcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT