Sequence
atgc intronic sequence ATGC exonic sequence...tccccacatgtactttatgtctttatcctcttatttatattccctatctatgagtattggataaatattaataatagtgtgaaatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
Basic information
species | Glycine max |
transcript | GLYMA20G00260.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
-tccccacatgtactttatgtctttatcctcttatttatattccctatctatgagtattggataaatattaataatagtgtgaaatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
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gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatc-attgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 10
tccccacatgtactttatgtctttatcctcttatttatattccc--tatctatgagtattggataaatattaataatagtgtga---aatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
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-----ttatggattgtgaaagttacatttttgaatgggagggaaaatgttcattgctattgactttgtcttttttactatttaccttaatgtgtctgctatgcagATTGTAGCAATCAATTCAGGTATTCAGCCAGGCTTAACAATGGTTGTGGGTCCACCTGGTACAGGAAAGACTGACACTGCTGTGCAGATCTTGAATGTTC
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 10
tccccacatgtacttt-atgtctttatcctcttattt-atattccctatctatgagtattggataaatattaataatagtgtga---aatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
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-----ttatagattgtgaaagctacattttttaatgggagggaaaatgttcattgctattgactctgtctttttgactatttaccttaatgtctctgctatgcagATTGGAGCAATCAGTTCAGGTATTCAGCCAGGCTTAACAATGGTTGTGGGTCCACCTGGTACAGGAAAGACTGACACTGCTGTGCAGATCTTGAATGTTCMapped 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|23051238|gb|BU577067.1|BU577067EST: ATCCTCAAGATCAGCCTAAACAAAATTCAGTTCGATTTACTCCCACCCAG GTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGG
genomic: ATCCTCAAGATCAGCCTAAACAAAATTCAGTTAGATTTACACCCACCCAGgtgaattcag ... tatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctatgagtattggataaatattaataatagtgtgaaatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
tattaat putative branch site (score: 2)
ttcttatc putative PPT
ataaatattaataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccccacatgtactttatgtctttatcctcttatttatattccctatctatgagtattggataaatattaataatagtgtgaaatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
tccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagtgtg