Sequence
atgc intronic sequence ATGC exonic sequence...tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggagcaaagacttataatagttagcatttacatttgaagCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
Basic information
species | Glycine max |
transcript | GLYMA09G34600.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G35600.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggagcaaagacttataatagttagcatttacatttgaagCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
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gtatttgaaacccattctctccataacattttcaagaatatgtttcacttaaggacatag--aatgattcaatgtgaaatgaagctaacatatacttgtatc-gtttttgaagCCGGGAGGTTTTCGACAAGTGGCAGGCTCAGAGGTGGTGGGGTGAGAACTATGACAGAATAGTTGAGCTTTACAATGTTCAAAGATTTAACCGACAAGCT
upper sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggag-caaagacttataatagttagcatttacatttgaa-gCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
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---gtatttgaactactc--aaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
upper sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggag-caaagacttataatagttagcatttacatttgaa-gCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
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---gtattttaactactc--aaaacaatctctatatcttcatgacattcaaagctggaacatgagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
upper sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggagcaaagactta--taatagttagcattt-acatttgaagCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
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-tttcatagaaactgg--gactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttaattatccagtaggagcaaagacttataatagttagcatttacatttgaagCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
agttaat putative branch site (score: 4)
aaagacttataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggagcaaagacttataatagttagcatttacatttgaagCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - ccatttg
- - - - - - - - - - - - - - - - - gttgttg