Sequence
atgc intronic sequence ATGC exonic sequence...tcttttctgactttaggtggatatgctatgcgtgcccaagtatatttggtgtaactagctgcttttgaaaataataatgatgattggctttttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAGGATTTGAGGAATGAAATTTTGAACTCTGAAAA
Basic information
species | Glycine max |
transcript | GLYMA20G37930.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37930.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34910.1 (Arabidopsis thaliana), 3'ss of exon 11
tcttttctgactttaggtggatatgctatgcgtgcccaagtatatttggtgtaactagctgcttttgaaaataataatgatgattggctttttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAGGATTTGAGGAATGAAATTTTGAACTCTGAAAA
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----------------gtgagtaatctctgt-------agta-agatgat-tacttctttcattaagtgaacagtattaaaagttgcaatttgtttgcagGATGTGGCAAAGAGTGTTACAAAGATTGCGGTTCGAGAGTCTCGAGCTCAGGATTTGAGGAATGAGATAATCAACTCTGAAAA
upper sequence: GLYMA20G37930.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0441g00010.t01 (Vitis vinifera), 3'ss of exon 10
tcttttctgactttaggtggatatgctatgcgtgcccaagtatatttggtg-taactagctgcttttgaaaataataatgat-gattggc-----tttttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAGGATTTGAGGAATGAAATTTTGAACTCTGAAAA
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---atggtaatggcatgggaata-gctgta--tggttatgtg-atttaatgctcaacagacgctagagaaagcacaaatcattgatcagccaaggtgggttttgcagGATGTTTCAAAGAGTGTGACAAAACTTGCTGTAAGAGAATCCCGAGCACAGGATCTGAGGAATGAAATTGTCAACTCTGAAAA
upper sequence: GLYMA20G37930.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0525g00010.t01 (Vitis vinifera), 3'ss of exon 4
tcttttctgactttaggtggatatgctatgcgtgcccaagtatatttggtg-taactagctgcttttgaaaataataatgat-gattggc-----tttttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAGGATTTGAGGAATGAAATTTTGAACTCTGAAAA
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---atggtaatggcatgggaata-gctgta--tggtcatgtg-atttaatgctcaacagatgctagagaaagcacaaatcattgatccgccaaggtgggttttgcagGATGTTTCAAAGAGTGTGACAAAACTTGCTGTAAGAGAATCCCGAGCACAGGATCTGAGGAATGAAATTCTCAACTCTGAAAAMapped 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|192332836|gb|FK026837.1|FK026837EST: TTCCCCTCCTCACCAAGAATGCAGTTGAATCTTTACGGTACAGGGCTGAG GATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAG
genomic: TTCCCCTCCTCACCAAGAATGCAGTTGAATCTTTACGGTACAGGGCTGAGgtaatttatt ... tttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAG
EST:
gi|192332835|gb|FK026836.1|FK026836EST: TTCCCCTCCTCACCAAGAATGCAGTTGAATCTTTACGGTACAGGGCTGAG GATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAG
genomic: TTCCCCTCCTCACCAAGAATGCAGTTGAATCTTTACGGTACAGGGCTGAGgtaatttatt ... tttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtgtaactagctgcttttgaaaataataatgatgattggctttttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAGGATTTGAGGAATGAAATTTTGAACTCTGAAAA
gtgtaac putative branch site (score: 3)
ctttttcttgc putative PPT
ttttgaaaataataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttctgactttaggtggatatgctatgcgtgcccaagtatatttggtgtaactagctgcttttgaaaataataatgatgattggctttttcttgcagGATGTTGCAAAGAGTGTAACTAGAATTGCTGTCCGAGAGTCACGAGCCCAGGATTTGAGGAATGAAATTTTGAACTCTGAAAA
- - ttctgac
- - - - - - - - - -gatatgc
- - - - - - - - - - - - - - -gcgtgcc
- - - - - - - - - - - - - - - - - - - - - - tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat