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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggatcctccaatccttttctgtttcaaatattgtataacaacaatgaagaccgttttcagaatgtgtgtttaatattctttatttatgattcattttgtcaatctgttttgttggtaatttgattttattttctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG

Basic information

species Glycine max
transcript GLYMA07G36610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 2
gtggatcctccaatccttttctgtttcaaatattgtataacaacaatgaagaccgttttcagaatgtgtgtttaatattctttatttatgattcattttgtcaatctgttttgttggtaatttgattttattttctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
                                  |||    | |  ||  |  | || ||    ||| |||   | |   | || ||  ||| |    ||     ||    |  |  |   || | |||| ||   | |   |||||  |  |||||||||| ||||||||||| ||||||||||| ||||| || || || | 
----------------------------------gtaatgtatctgtgttg--cattctc---ctgtttgtcacagacaatatagttgagatcc----tggagtcctagaatactactggctt-actttactta--tcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC

upper sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 2
gtggatcctccaatccttttctgtttcaaatattgtataacaacaatgaagaccgttttcagaatgtgtgtttaatattctttatttatgattcattttgtcaatctgttttgttggtaatttgattttattttctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
                                                         ||  |     |   ||||| | || | | ||   |||||||  |   | ||    |   ||  |   || |||  |  |||||   ||||  | ||||||||||| || || ||||| ||||||||||| |||||||| ||||| ||
------------------------------------------------------aacttaggctcagggacttaatgtgctctttgtaattttcatttc-tatttatgacaaggcagtg-taaaatgttaaatcatttggcattgttgct-atgcagGAAATTGATTTAAAGAATCACAAATGGGGTCATTATTTCATTTGCGG
















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|209713259|gb|BW684346.1|BW684346
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
EST: gi|6070813|gb|AW100200.1|AW100200
EST:     TGAATGGTGAAAAATATTCACTCTGTACTTATCCTGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
EST: gi|213589192|gb|DB957724.1|DB957724
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
EST: gi|19348464|gb|BM892996.1|BM892996
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
EST: gi|213603198|gb|DB960461.1|DB960461
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCTGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctgttttgttggtaatttgattttattttctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
                 atttgat  putative branch site (score: 5)
                                         tgtttttc  putative PPT
               taatttgattttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggatcctccaatccttttctgtttcaaatattgtataacaacaatgaagaccgttttcagaatgtgtgtttaatattctttatttatgattcattttgtcaatctgttttgttggtaatttgattttattttctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC