Sequence
atgc intronic sequence ATGC exonic sequencegtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
Basic information
species | Glycine max |
transcript | GLYMA13G20240.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
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------------------------------------------gtgatgggttataattcctttggcaacttttct--tataatt---gaatttacaaaa----gttgtcttaaatagataccagtgttgtgagc-atatcacccccgtatgatactgtttattgacattgtgattgta-----ttgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctccttta-attcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
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------------------------------------gtaactggatctaaatcct-ttgacaaatgatcttccctattgcatttgtagg------aaaataatattctgtg--ttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgta-tgctaacattgcga--ttggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 8
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
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---------------------------------------------------------------------------------------------acatgatatcatttcttctagttctttttccttttgtaaaatattattactccctttgaaaagagagtggtataatag-acaacaaaatgat--gctgaacagCGTGGATGGAAAATATATTTTGACTGGAGGTGAGGATGATCTAGTTCAAGTTTGGAGTATGGAAGATCGGAAGGTTGTGGCATGGGGTGAGGGACACAAC
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ38679 (Selaginella moellendorffii), 3'ss of exon 8
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
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-----------------------------------------------------------------------------------------------------------------------------gtaaacagcgcttgtgtatttggaatacttttcttatatcttctctcttctt------tcctctctcttagCTCGGATGGGAAGTACGTGTTGGCTGGTGGAGAGGATGATTTAGTCCAAGTCTGGAGCATGGAAGACCGGGCGGTTGTTGCCTGGGGAGAGGGTCACAAT
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ31470 (Selaginella moellendorffii), 3'ss of exon 8
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
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-----------------------------------------------------------------------------------------------------------------------------gtaaacagtgcttgtgtatttggaatacttttcttatatcttctctcttctt------tcttctctcttagCTCGGATGGGAAGTACGTGTTGGCTGGTGGAGAGGATGATTTAGTCCAAGTCTGGAGCATGGAAGACCGGGCGGTTGTTGCCTGGGGAGAGGGTCACAATMapped 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|9204238|gb|BE330462.1|BE330462EST: ATATGTGGTGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCTTGGAG CATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGT
genomic: ATATGTGGTGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCTTGGAGgtgaggcata ... gttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGT
EST:
gi|51337326|gb|CO981192.1|CO981192EST: ATATGTGGTGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCTTGGAG CATGGATGGAAAGTATANNTTGACGGGGGGAGAGGATGATTTAGTTCAAGT
genomic: ATATGTGGTGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCTTGGAGgtgaggcata ... gttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
ctttaat putative branch site (score: 4)
tctgtttt putative PPT
tataatgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA