Sequence
atgc intronic sequence ATGC exonic sequence...ccaataataccattcactctattgatcaaatttaccggcatatgatcatttgaaaagttgttttattatttctctaaaagtcatttgaatttctttgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT
Basic information
species | Glycine max |
transcript | GLYMA07G32850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0094g00730.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------------------ccaataataccattcactctattgatcaaatttaccggcatatgatcatt-tgaaaagttgttttattatttctctaaaagtcatttgaatttctt--------tgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT------
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gtgagtgtgttcttcacttcttacaaaagtttacggaatgttcataccatctagtagaaaatgacgagtgtctatgttcattgt-ttcatcctaaccagtagtgtctaacccttgtgaaaagacggatc-cgaattgtaagtacctaatcaaaatttcttctgtttaatgtagGGAGATTAAGAATACAAAGAAGACTTCTAGCTCTCCTCGCAAGGTGCA------AGTAACCCATTCAATGCCACCACACAAGATTGAGATTTTCAAATCCATGGAG
upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0094g00650.t01 (Vitis vinifera), 3'ss of exon 3
ccaataataccattcactctattgatcaaatttaccggcatatgatcatttgaaaagttgttttattatttctctaaaagtcatttgaatttctttgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT
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---gtaacccactcaatgccaccacacaagattga-gattttcaaatccatggagaattgggttg----------aggagaagttttaattcacctgaagCCAGTTGAGAAAT---------------------------------------------------------------------------------------
upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------------------ccaataataccattcactctattgatcaaatttaccggcatatgatcatt-tgaaaagttgttttattatttctctaaaagtcatttgaatttctt--------tgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT------
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gtgagtgtgttcttcacttcttacaaaagtttacggaatgttcataccatctagtagaaaatggctagtgcctatgttcatagt-ttcatcctaaccagtagtgtctaacccttgtgaaaagacggatc-cgaattgtaagtacctaatccaaatttcttctgtttaatgtagGGAGATTAAGAATACAAAGAAGATTTCTAGCTCTCCTCGCAAGGTGCA------AGTAACCCACTCAATGCCACCACACAAGATTGAGATTTTCAAATCCATGGAG
upper sequence: GLYMA07G32850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0094g00740.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------ccaataataccattcact---------ctattgatcaaatttaccggcatat---gatcatt-tgaaaagttgttttattatttctctaaaagtcatttgaatttctttgtagAGAGGTTGAAAA--TATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT------------
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gtgagtgtgttcttcacttcttacgaaagtttacggaatgttcataccatctagtagaaaatgacaagtgtctatgttcattgtttcattctaaccattgtgaaaagacggatc-cgaactgtaagtacctaatccaaatttcttctgtttaatgtagGGAGGTTACTAAGAAGACTTTTAGCTCTCCTCACAAGA------TTCAAGTAACCCACTCAATGCCACCACACAAGATTGAGATTTTCAAATCCATGGAGAATTGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|20811946|gb|BQ296424.1|BQ296424EST: CTCAGATCTCCCCGCTTCCGCATGGCTTCCACCCTCCGCTCCGGTTCCAA AGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGT
genomic: CTCAGATCTCCCCGCTTCCGCATGGCTTCCACCCTCCGCTCCGGTTCCAAgttagtccct ... ttctttgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgaaaagttgttttattatttctctaaaagtcatttgaatttctttgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT
ctctaaa putative branch site (score: 3)
tttctttgt putative PPT
aaaagttgttttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaataataccattcactctattgatcaaatttaccggcatatgatcatttgaaaagttgttttattatttctctaaaagtcatttgaatttctttgtagAGAGGTTGAAAATATTAAGAAGCCATTCACTCCTCCCAGAGAAGTGCATGTTCAAGTAACCCACTCTATGCCTCCCCAGAAGATTGAGATTTTCAAATCT
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