Sequence
atgc intronic sequence ATGC exonic sequencegtaatattatagcgtcttctgttgcatttttcatattctgttactggccttttgaccccattaaatatgattttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
Basic information
species | Glycine max |
transcript | GLYMA13G31550.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
gtaatattat----agcgtcttctgt---tgcatttttcatattctgttactggccttttgaccccattaaatatgattttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
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gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 5
----------gtaatattatagcgtcttctgttgcatttttcatattctgttactggccttttgaccccattaaatatg-attttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
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gtttgttcatttaacctgaattcagctcttctcctattgataatgcctt--tgtttactggctaacttaattcaatttataatgtttcagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTTAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGAGAGTGGG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 8
--------gtaatattatagcgtcttctgttgcatttttcatattctgttactggccttttgaccccattaaatatg-attttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
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gtttgttcttttaatctgaatttcagatgttctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatattatagcgtcttctgttgcatttttcatattctg-ttactggccttttgaccccattaaatatgatttttt-cagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
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gtgagtttattgtgacttatctt----tttaattattctgattggaatcgagttgttcacctttaatctcttctttgacagAGATATGGTCCGCCTCCTTCTTACCCACATCTGAAAATTCCTGGTTTGAATGCTCCTATTCCAATTGGAGCTAGCTTTGGTTTTCATGCTGGCGGCTGGG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 1
---------gtaatattatagcgtcttctgttgcatttttcatattctgttactggccttttgacccca-ttaaatatgattttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
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gtcagatgagctaatttctcgcaattgattttgacctttacagaaccttcaactttgttttttcctttagctgactgtttatttttcagAGATATGGTCCGCCACCATCATATCCACATCTGAAAATCCCTGGGCTGAATGCTCCTATTCCTCCTGGTGCTAGCTTTGGTTATCATCCTGGTGGTTGGGMapped 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|24136279|gb|BU926789.1|BU926789EST: CTCTTGGTATGCCTGAAGGTTCTCCTCCTCCTTGGCTTATTAATATGCAG AGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAAT
genomic: CTCTTGGTATGCCTGAAGGTTCTCCTCCTCCTTGGCTTATTAATATGCAGgtaatattat ... attttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttttcatattctgttactggccttttgaccccattaaatatgattttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
ttttgac putative branch site (score: 3)
ttttttc putative PPT
attaaatatgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatattatagcgtcttctgttgcatttttcatattctgttactggccttttgaccccattaaatatgattttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA