Sequence
atgc intronic sequence ATGC exonic sequencegtaatttatctaattttgatattattattgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttctcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaatatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
Basic information
species | Glycine max |
transcript | GLYMA15G11890.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 4
gtaatttatctaattttgatattatta-ttgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttc-tcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaatatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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gtaagcgttttttttttaattttgtgaactgagcaataacttggttggtagacttccc--actgaggaggccacccctgagaattagtttcagggagttccctggccag--ctagggttttgggtactccacttttttaatacaaagcc----atgaaatgtcatctccaactctctcatgtagcttttgttat-tgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGTGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 11
gtaatttatctaattttgatattattattgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttctcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaatatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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-------------------------------------------------------------------------------gccagggaatgtcatctccctgtggtggtttt----ttctattaattttgcgtttccaaatttttctttccaactctctcatgca---------------gcttctttgctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatttatctaattttgatattattattgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttctcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaa---tatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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-----------------------------------------------------------------------------gtaagttacgcaatttgttctttcagttaa--ccaaatcgttat--ataatacattgcttatttattgatgtgaataatacaagcttgatttatggtttgta---atcaacttgaa---tacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 11
gtaatttatctaattttgatattattattgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttctcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaatatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
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gta-tgtaccatcttttgatgaaaa-aggatatagcta-ttttgagtcacat--atttcaattacaag-------taatgacatgatattcttactcaaattgttgaaccta---cccccacaacaatttatgttagttatgac--------------actatgtt----ttgtttctgg--catccctgatgtgcagATATGAAGGGAGGTGTGGTTTTCCAACTAACTTCGATGCTGCCTACTGCTATGCATTGGGTTTTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGMapped 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|21602004|gb|BQ612335.1|BQ612335EST: CAAGAAGGCAAATACAATGGCGAATTTAAAGGGCAATCCCACTTTTTTGG TTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
genomic: CAAGAAGGCAAATACAATGGCGAATTTAAAGGGCAATCCCACTTTTTTGGgtaatttatc ... aaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
EST:
gi|17021166|gb|BM092200.1|BM092200EST: CAAGAAGGCAAATACAATGGCGAATTTAAAGGGCAATCCCACTTTTTTGG TTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
genomic: CAAGAAGGCAAATACAATGGCGAATTTAAAGGGCAATCCCACTTTTTTGGgtaatttatc ... aaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttaaatgacttaatatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
tactgac putative branch site (score: 1)
taaatgacttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttatctaattttgatattattattgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttctcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaatatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA