Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
Basic information
species | Glycine max |
transcript | GLYMA17G04270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
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----------------------------------------------gtaagtacctctaat----gtattcaaact-acatttattcag-----tgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
upper sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
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-----------------------------------------gtgagtttttccttctctctttttacatgctagcttgtttgtgttaag-------cttattctgat-------gcattgcttttcttttt--------agGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
upper sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17330.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
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-----------------------------------gtgagtcgattcttcccctttgt--cccttgtgc--gaatgtgtttgcattcata--------ctttgtgctcatgctgatgtagtgcttcctt----cgttttagGTCAATTCCAGTGGTCTGTTCTGTGGCGTGGCTGAGATGACCGGTCCAGTTTCCTTCGACCGAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
upper sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaac-ttatgtgcatct-ggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
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gtgagttt-tgtcctctctcctctcctagttggctatggacc---ataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttc--atacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAAMapped 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|11412067|gb|BF424078.1|BF424078EST: TAAGAGAATTGCTTCTTGAAATTTTGGAAGCTGCCCTATCTNTCTTTCCTTTTCT
genomic: TAAGAGAATAGCTTCTGGAAATTTTGGAAGCTGCCCTATCTTTCTTTTCTTTTCTgtgagtttac ... tgcaat
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
tgctgac putative branch site (score: 2)
cattgttttccttttt CT-rich tract
attgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA