Sequence
atgc intronic sequence ATGC exonic sequencegtaaccaagtgcagaaattttggaattgcaagtagatctctgttatttctgcaactgtttgacatctaggaagctaatgctaagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
Basic information
species | Glycine max |
transcript | GLYMA09G40480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------gtaaccaagtgcagaaattttggaattgcaagtagatctctgttatttctgcaactgtttgac-atctaggaagctaatgctaagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
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gtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttgcatatttgat-tttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaccaagtgcagaaattttggaattgcaagtagatctctgttatttctgcaact-gtttgacatctaggaagctaatgc---taagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
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gtaaaagtttacctaaagtttg-attcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 3
gtaaccaagtgcagaaattttggaattgcaagtagatct--ctgttatttctgcaactgtttgacatcta-ggaagctaatgctaagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
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gtaaatgcaaggcaaccttttggg--tgcaagcagtactatcttctgttctttcaattacccagttctcatggaatctaatgtaaaattcctggcagGAAGGTATAGCTCTTTTCAATCGGAAGCCTAAAAAAGGAATTGAGTTCCTTATTAATGCAAATAAGGTGGGAAACACACCAGAGGAGATAGCAGCTTTCCMapped 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|208242213|gb|GE037823.1|GE037823EST: CGCCGGGCTTATAAACTGAAACTTCAG GAAGGTATATCACTTTTTAACAGGAAG
genomic: CGCCGGGCTTATAAACTGAAACTTCAGgtaaccaagt ... tttatggcagGAAGGTATATCACTTTTTAACAGGAAG
EST:
gi|193581971|gb|FK536896.1|FK536896EST: CGCCGGGCTTATAAACTGAAACTTCAG GAAGGTATATCACTTTTTAACAGGAAGCCG
genomic: CGCCGGGCTTATAAACTGAAACTTCAGgtaaccaagt ... tttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttatttctgcaactgtttgacatctaggaagctaatgctaagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
agctaat putative branch site (score: 3)
taagtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccaagtgcagaaattttggaattgcaagtagatctctgttatttctgcaactgtttgacatctaggaagctaatgctaagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT