Sequence
atgc intronic sequence ATGC exonic sequence...agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
Basic information
species | Glycine max |
transcript | GLYMA13G43680.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 23
agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttg-------cagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
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gtgaccattttttag-ctgcaatcagtgttctaggattcttacaaaggtt--aaagctaacatgtatttttctt-ttcattttccttcccatgcttggactacttagCTGGATATGGCTGAGGAATGCATGAGGCATGCTATGGATTTGAGTGGTCTGCTGCTGCTTTATTCTTCATTGGGAGATGCAGATGGAATGATGAAGCTGG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
-----agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
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caatgccaatgagctttc-ttctagcttttgcgga-ttcattgctgatatctactacttac-taagtgattctcttgcatttg--tgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 19
----agaataa-gttatgattctagaatgagggaacttaaatgt-tgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
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tgtgggagcaacagcaaaatctctgtttctcgtctcctggatttgtctttgatgtggggatttccaactaactctttccgtttt------tatgtcatcatgacagCTGCAAATGGCTGAGGAATGCATGAAGTATGCGATGGATTTGAGTGGTTTGTTACTTCTTTATTCTTCTCTGGGAGATGCTGAAGGTGTAACAAAACTTG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
-agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
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cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcat-tgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 19
agaataagttatgattctagaatgagggaacttaaatgttga----ttcttgttggaaacctctcttgacccgttgtagctcaccgtattttcca------ttcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
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---------tatg-tcctagatcatattgcttcagatgaccaccactccccttccccctcctcttttttattccaatgtcttaatgtatgtactggaattgttaatgcagTTTGAGATGGCTGAGGAATGCCTTTTACACGCCATGGACTTGAGTGGTTTGTTGCTCCTCTATTCTTCTTTTGGTGATGCCAATGGAATATCAAAACTTGMapped 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|298199623|gb|HO043500.1|HO043500EST: GCGAGCCTAAATGGAAGCAGTTGGGAGAATTAGCTATGTCTACTGGAAAG TTAGAAATGGCT
genomic: GCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAGgtgttttcta ... attcttgcagTTAGAAATGGCT
EST:
gi|151398221|gb|EV268099.1|EV268099EST: GCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAG TTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTG
genomic: GCGAGCCTAAATGGAAGCAATTGGGAGAATTAGCTATGTCTACTGGAAAGgtgttttcta ... attcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
agctcac putative branch site (score: 3)
tattttccattctt putative PPT
tatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA