Sequence
atgc intronic sequence ATGC exonic sequence...gaaattagtgaagggaataatatgcttggtttgaagaacaaatatttttgtgcactttgataatttggataacatttaactaaaatacatacttatttagATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAAGGAGGTCCTGAAACATTTCGTGGAATTTTTATTCGTGCCCCTGCAATTC
Basic information
species | Glycine max |
transcript | GLYMA01G28830.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G28830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G023528_T03 (Zea mays), 3'ss of exon 4
--------------------gaaattagtgaagggaataatatgcttgg----tttgaagaacaaatattt-ttgtgcactttgataatttggataacat--ttaacta-aaatacatacttatttagATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAAGGAGGTCCTGAAACATTTCGTGGAATTTTTATTCGTGCCCCTGCAATTC
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gtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAAGGAGGGAATGATACATGCCGCGGTGTATTTATACGGGCACCTGCTATAT
upper sequence: GLYMA01G28830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G023528_T02 (Zea mays), 3'ss of exon 4
--------------------gaaattagtgaagggaataatatgcttgg----tttgaagaacaaata-tttttgtgcactttgataatttggataacat--ttaacta-aaatacatacttatttagATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAAGGAGGTCCTGAAACATTTCGTGGAATTTTTATTCGTGCCCCTGCAATTC
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gtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagACTGTTTCTCTTGCAGCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAAGGAGGGAATGATACATGCCGCGGTGTATTTATA----------------Mapped 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|21637681|gb|BM107836.1|BM107836EST: TGGTTGGTGGACTTGATTGTACAGTGCATAGAAATTTCTTTGGCAGCCAG ATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAA
genomic: TGGTTGGTGGACTTGATTGTACAGTGCATAGAAATTTCTTTGGCAGCCAGgtaaatgcat ... acttatttagATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtgcactttgataatttggataacatttaactaaaatacatacttatttagATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAAGGAGGTCCTGAAACATTTCGTGGAATTTTTATTCGTGCCCCTGCAATTC
aactaaa putative branch site (score: 2)
cttattt putative PPT
ataacatttaactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaattagtgaagggaataatatgcttggtttgaagaacaaatatttttgtgcactttgataatttggataacatttaactaaaatacatacttatttagATTCAAAGCTTTGAGGCAGAGCTTTCAGTGCCAGAGCTCGTCTCCAAAGAAGGAGGTCCTGAAACATTTCGTGGAATTTTTATTCGTGCCCCTGCAATTC
- - - -gtgaagg
- - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - - gaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - tgcactt