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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggatcctccaatccttttttgttttaaatactactgtataacaatgaagaccgttttcagaaatgtgtgtttaatatttttttctttatgattcattttgtcaataagatcgtgctatgttttgttggtaatttgatctgatattctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG

Basic information

species Glycine max
transcript GLYMA17G03990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 2
gtggatcctccaatccttttttgttttaaatactactgtataacaatgaagaccgttttcagaaatgtgtgtttaat-atttttttctttatgattcattttgtcaataagatcgtgctatgttttgttggtaatttgatctgatattctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
| | || || | | | | |||| | | | |||| || | || | ||| ||| || ||||| || | | | | ||||||||||||||||| ||| | || |||||||||||||| || ||||| || |||||
---------------------------------------------------------tgccatgatccgtctgaagttgctgttttttcttagcttcagttatttgat------------tatttctttgatatattgatttggttgttgataa--atatttttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG

upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 2
gtggatcctccaatccttttttgttttaaatactactgtataacaatgaagaccgttttcagaaatgtgtgtttaatatttttttctttatgattcattttgtcaataagatcgtgctatgttttgttggtaatttgatctgatattctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
| | | ||| | ||| | | ||| | | | | | | ||||| || | | | || | | || | | | ||||| | |||||||||| ||||||||||| ||||||||||| ||||| || ||||| |
-----------------------------------------------------------gtaatgtatctgtgttgcattctcctgtttgtcacagacaatatagttgagatcctggagtcctagaatactactggcttactttacttatcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
















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|298199023|gb|HO042386.1|HO042386
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|209699970|gb|BW661199.1|BW661199
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|213611707|gb|DB969095.1|DB969095
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|207782813|gb|GD752396.1|GD752396
EST:     AATGGTGTAAAAATTATTCACTTTGTACTTATCCCGCCGATCCTCTCTAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: AATGGTG-AAAAA-TATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|298190390|gb|HO032511.1|HO032511
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|192321624|gb|FK013968.1|FK013968
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|13481495|gb|BG510838.1|BG510838
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|19453433|gb|BM954843.1|BM954843
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|213597925|gb|DB958306.1|DB958306
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
EST: gi|209712397|gb|BW671249.1|BW671249
EST:     TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAG                         GAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
genomic: TGAATGGTGAAAAATATTCACTTTGTACTTATCCCGCCGATCCTCTCCAGgtggatcctc ... tttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatgttttgttggtaatttgatctgatattctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
                      atctgat  putative branch site (score: 4)
 tgtttttc  putative PPT
 taatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggatcctccaatccttttttgttttaaatactactgtataacaatgaagaccgttttcagaaatgtgtgtttaatatttttttctttatgattcattttgtcaataagatcgtgctatgttttgttggtaatttgatctgatattctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG

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