Sequence
atgc intronic sequence ATGC exonic sequence...ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
Basic information
species | Glycine max |
transcript | GLYMA16G01230.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
ataaaaataagcttaaacaaata-ggacctatgttcatactaagtctgatc-ccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
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------gtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 5
ataaaaataagcttaaacaaataggacctatgttcatactaagtctg-atcccctttgggaacttttggctaaggtatagccttt--ttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
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--------------------gtaagttttgactttttttaagtgttgcattttgtttgtatgtttttgaggatactcaatgttttagtttccatgagttgcagGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTC
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 5
ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttt-tggctaaggtatagcctttttct---tttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
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------gttggttcaca-atcttatgcttgatttcttgctaaaacag---tattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
-------ataaaaataagcttaaacaaataggacctatgttcatacta-agtctgatccc------ctttgggaacttttggctaaggtatagcctttttcttt--taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
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gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCMapped 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|209725663|gb|BW663152.1|BW663152EST: TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG GTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAGgttagttcag ... taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
EST:
gi|26058275|gb|CA801189.1|CA801189EST: AGAGAGAGGATACGTCAG GTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
genomic: AGAGAGAGGATACGTCAGgttagttcag ... taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTA
EST:
gi|298165726|gb|HO008697.1|HO008697EST: TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG GTCATTACAACATTTTTGTTGGCGATCT
genomic: TATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAGgttagttcag ... taatttgcagGTCATTACAACATTTTTGTTGGCGATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
ttttaat putative branch site (score: 3)
cctttttcttttaatt CT-rich tract
tttttcttttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -aaaataa
- - - - - - - aaacaaa
- - - - - - - - - - - - - cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - tcccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg