Sequence
atgc intronic sequence ATGC exonic sequencegtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
Basic information
species | Glycine max |
transcript | GLYMA02G09390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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------------------gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaacca---tggcacactt-agGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 6
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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gtaatgcat--gatgccctgagca----cacgttcctgatg--tttattctacctaatag-aatggtaattgatgcca-atttacacttatgc--------tgatgtc----agGAAGAAAGGAAAACTCTTGATCGTGAACTAGCTCGTGCGAAGGTTTCGGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATA
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 6
---gtaacttgttaaaagtcttcagcatgt----tcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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gtaacaacctattctttgactattgcatatgtcatcatgtcttcatgagctct-tccccccttctataggaac-agttcac-tcatgcttattt----aacatttat--gatcattaccagGACCAAAAAAAGACACTTGAATGTGAACTTGCTCGTGCAAAAGTTACAGCAAACAGGGTTGCTGTTGTGGTTGCCAACGAGTGGAAAGATTCTAATGACA
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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---------------------gtaagttaatacatttccgaaaaaagaagtatagaatctttactcaactgatgaaggaat--atttct---tgctctact------tttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttat-ttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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-----------------------gtaactaaacac--acttcataaagtctctaatttcttgtcacaa--caattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
gtaacttgttaaaagtcttcagca--tgttcaa-actcccatttgctttattcttcattatattgactctagtta--agatcatatttatttttgcatggtttatttgacattcttt---------------agGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggctt-atatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 6
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
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---------------------------------------------------gtagtgccgccagccacctttgggtcgcactcacccc-acattgtctttttaccatt----agGAAGAGAAACGGACGCTTGAGCGGGAACTGGCGCGTGCCAAGGTAACAGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACAMapped 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|193730375|gb|FK663473.1|FK663473EST: CAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAAT GAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCA
genomic: CAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaacttgtt ... cattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCA
EST:
gi|14990947|gb|BI316620.1|BI316620EST: CAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAAT GAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCA
genomic: CAGCTGCAAATGCAGTGAGGGATTATCAGCGGAAAGTTCAAGAAATGAATgtaacttgtt ... cattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
cattcttt CT-rich tract
tagttaagatcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttatttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG