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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacttcagcatacttttatgtgaatagtttaaaaacaagtttgttttgctttatcattttccccgtccttttcataataattcttaattggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATAGACGAAGAAAAGGTTATGATGGAGTCACTGATGTGCCTCCGAAGGGCCG

Basic information

species Glycine max
transcript GLYMA04G42670.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 11
-aaacttcagcatacttttatg---tgaatagtttaaaaacaagtttgttttgctttatcatttt-ccccgtccttttcataataattcttaattggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATAGACGAAGAAAAGGTTATGATGGAGTCACTGATGTGCCTCCGAAGGGCCG
   | || | | |   ||||     |   |  ||      ||    |||| || |   |||  || | || || |  |  |  | ||| |   | | |     ||||||||||||||||  ||||||| |||||||  | || |||||||||||| || |||||||| || |||||||||||||||||||| || ||| |||| |
ttcaatttaacttgggtttacaatctttttccttccctttcattcctgttatgatgcctcagattgctccatcttccttgt--ttattttccctggat---ctagGTTTCTGGTGAATACTCAATGATCAAGGCTGGTGCTGTTCTCAAAATGATTGATGAAGAAAAAGTCATGATGGAGTCACTGATGTGTCTTCGACGGGCTG
















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|7028233|gb|AW458016.1|AW458016
EST:     TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|7691223|gb|AW759354.1|AW759354
EST:     TCATAAGGCTGCTCANGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|207833752|gb|GD807627.1|GD807627
EST:     TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|6455519|gb|AW186202.1|AW186202
EST:     TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|193306739|gb|FK270089.1|FK270089
EST:     TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|208188505|gb|GD983189.1|GD983189
EST:     AAGGCTGCTCAGGGATTAATTTCTTCCTTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: AAGGCTGCTCAGGGA-TAA-TTC-TCC-TTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|23057473|gb|BU578156.1|BU578156
EST:     TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGGCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
EST: gi|17022525|gb|BM093559.1|BM093559
EST:     TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAG                         GTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA
genomic: TCATAAGGCTGCTCAGGGATAATTCTCCTTTGCCAATTGCAGCATACCAGgttcttttct ... ggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctttatcattttccccgtccttttcataataattcttaattggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATAGACGAAGAAAAGGTTATGATGGAGTCACTGATGTGCCTCCGAAGGGCCG
                                     tcttaat  putative branch site (score: 3)
                        ttttcataataattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacttcagcatacttttatgtgaatagtttaaaaacaagtttgttttgctttatcattttccccgtccttttcataataattcttaattggtggaacagGTTTCTGGTGAATATGCAATGATAAAGGCTGCCGGTGCTCTCAAAATGATAGACGAAGAAAAGGTTATGATGGAGTCACTGATGTGCCTCCGAAGGGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - gcatact
- - - - - - - - - - - - - - - - aaaacaa