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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTATCAACAGTCCCCAAACCCTCGTCTTAACGAGAGGATTCTTTCATCCATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatgtaattgtaaaattgtgacatcttaatgttttgatcgtgatgtatttcttttttcttactttattttgtatgttaactgtattttctccacaatgcag

Basic information

species Glycine max
transcript GLYMA13G19500.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
AGCTATCAACAGTCCCCAAACCCTCGTCTT-AACGAGAGGATTCTTTCATCCATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatgtaattgtaaaattgtgacatcttaatgttttgatc---gtgatgtatttcttttttcttactttattttgtatgttaactgtattttctccacaatgcag
  |   || |   |   |    |  | ||| ||||| ||||| || |||||||| ||||||||    |||||||||||||| ||||| ||||| ||||||||||   | |  |      |  |||  | ||  | |    ||||||   |  || |    |       | | || || ||| ||     | |                   
-ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgta--ttgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag-------------------

upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 2
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 2
AGCTATCAACAGTCCCCAAACCCTCGTCTTAACGAGAGGATTCTTTCATCCATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatgtaattgtaaaattgtgacatcttaatgttttgatcgtgatgtatttcttttttcttactttattttgtatgttaactgtatt---ttctccacaatgcag
    |  ||||     ||   |||  |||||| |||||||| ||||| |||||       |||   || ||||||||||| ||||| ||||| ||||||||||||||||             | |  | | ||  ||  |  |   | || |  || ||||||  || |   | || ||  ||   ||  |    |||       | |||
GTTGAGAAACATGTTTCACTTCCTACTCTTAATGAGAGGATACTTTCGTCCATGAGTCACAGATCAGTAGCTGCACACCCATGGCATGATCTCGAGATAGgtaagctatacgtaaaggtttctttttcttttttttggctctaagatcatttcattgttttttagtaataactcttataccttttttgcttcgcattcctttgtttacag

upper sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 2
AGCTATCAACAGTCCCCAAACCCTCGTCTTAACGAGAGGATTCTTTCATCCATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatgtaattgtaaaattgtgacatcttaatgttttgatcgtgatgtatttcttttttcttactttattttgtatgttaactgtattttctccacaatgcag
| || ||| ||   | || |||| | |||||| || |||||||||||||||||  || ||||    |||||||||||||| ||||| ||||||||||||||||     | |  ||||||        ||| || |    || ||  | |  | | || |||||  || |     || |||  | ||  | |||  | |  |||||||
AACTCTCATCAACACTCACACCCACCTCTTAATGAAAGGATTCTTTCATCCATGACCCGGAGGGCTGTTGCTGCACACCCCTGGCATGATCTTGAGATAGgtacctacttttgttgtaacg------catgttga---gttaattctta-atgtctcctttttactagtg-gccttttattatgacattttttatttc--aatgcag

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|298184004|gb|HO029217.1|HO029217
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|12489759|gb|BG043280.1|BG043280
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|26269126|gb|CA820189.1|CA820189
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|192330021|gb|FK020837.1|FK020837
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|13479768|gb|BG509111.1|BG509111
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|19346407|gb|BM891287.1|BM891287
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|37996937|gb|CF808526.1|CF808526
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|298181507|gb|HO022946.1|HO022946
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|298169347|gb|HO020707.1|HO020707
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|6133848|gb|AW132241.1|AW132241
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCCGAAGCT-CAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGA-CCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|9565429|gb|BE474938.1|BE474938
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|7587913|gb|AW703719.1|AW703719
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|12489693|gb|BG043214.1|BG043214
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAAATCTTC
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTC
EST: gi|8403914|gb|BE059548.1|BE059548
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|192324146|gb|FK017877.1|FK017877
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|213593665|gb|DB971687.1|DB971687
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|4396573|gb|AI495570.1|AI495570
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAA-GATCTTCA
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCA
EST: gi|209719745|gb|BW672120.1|BW672120
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|298178505|gb|HO024240.1|HO024240
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGC
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|209701982|gb|BW664582.1|BW664582
EST:     CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT
EST: gi|17154018|gb|BM143951.1|BM143951
EST:     CATTTCCAGGAGACACGTTGCTGCACACTCGTGGCACGATCTTGAGATAG                         GACCCGAAGCTCCAAAGATCTTCAACTGT
genomic: CATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatg ... cacaatgcagGACCCGAAGCTCCAAAGATCTTCAACTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTATCAACAGTCCCCAAACCCTCGTCTTAACGAGAGGATTCTTTCATCCATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatgtaattgtaaaattgtgacatcttaatgttttgatcgtgatgtatttcttttttcttactttattttgtatgttaactgtattttctccacaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC