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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcaccctttctttatctttgtctatttatttatttatttcctaggacttcaatttcttcttatttatttgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG

Basic information

species Glycine max
transcript GLYMA03G33260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g02880.1 (Oryza sativa), 3'ss of exon 3
gtaagttgtcaccctttctttatctttgtctatttatttatttatttcctaggacttcaatttcttcttatttatttgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG
                                                                          | ||  ||    |     ||  | | |   |        | | |||||  |  | ||         ||   || || || |  |||  |||  | |      |||||| || |||||||| || |||||||| || ||||| || ||| | |||||  |||||||||||||||| || ||| |||| || ||||| ||||||
-------------------------------------------------------------------------gtatgtgaattattcttccctcatttttttctctcttttctaaattgtaccttttagttca---caagtccaacatttttcggatgtctcttttacc----aaacagGAGTTCAGTGATCCCCGTGATGCTGAGGAAGCAAGGTACAACCTTGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGG

upper sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g17710.1 (Oryza sativa), 3'ss of exon 3
gtaagttgtcaccctttctttatctttgtctatttatttatttatttcctaggacttcaatttcttcttatttatttgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG----
                                            | |   |  |||||    || | || ||||||   |||  | |  ||| |  ||  | |||    |   |   ||||  |      ||||| | || | ||    |   | | | |   |||| |       |||||| || |||||||| || ||||||||||| ||  | |||||| | |||||  |||||||||||||||| || ||| |||| || ||||| |||||     
-------------------------------------------gtatgtgaatacttc--cctcatttt-tttattgcgtaacttctctctttt--taagttcttatgaggtgtattttgttcaca----tatgagtcctatatt----ttgcgacatctattttacca------aacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGAGTAA

upper sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
gtaagttgtcaccctttctttatctttgtctatttatttatttatttcctaggacttcaatttcttcttatttatttgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG
                                            | |   |  |||||    || | || ||||||   |||  | |  ||| |  ||  | |||    |   |   ||||  |      ||||| | || | ||    |   | | | |   |||| |       |||||| || |||||||| || ||||||||||| ||  | |||||| | |||||  |||||||||||||||| || ||| |||| || ||||| ||||| 
-------------------------------------------gtatgtgaatacttc--cctcatttt-tttattgcgtaacttctctctttt--taagttcttatgaggtgtattttgttcaca----tatgagtcctatatt----ttgcgacatctattttacca------aacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA

upper sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
gtaagttgtcaccctttctttatct-ttgtctatttatttatttatttcctaggacttcaatttcttcttatttatt-tgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatg---atttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG
                    ||| | |   | |||| || || |||||| |          ||    |||  ||||  |  |  | | |   |     ||| |   |  || | |    || |||||| || ||     || |  |  |  | || || | |  | |  |  |   | |  |||||| || |||||||| |||||||||||||||||||||||||||||  |||| || ||| |||||||||||||||| |||||||||||||| ||||||
-------------------gtatgtatcaaccatttgttcatctatttctt----tcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG

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|298189291|gb|HO037694.1|HO037694
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|298170069|gb|HO018693.1|HO018693
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|213589600|gb|DB965816.1|DB965816
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|151403736|gb|EV273546.1|EV273546
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|192324223|gb|FK017954.1|FK017954
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|213597756|gb|DB960313.1|DB960313
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|193406622|gb|FK375581.1|FK375581
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATG
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATG
EST: gi|298193736|gb|HO040384.1|HO040384
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGTTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
EST: gi|192334590|gb|FK025179.1|FK025179
EST:     AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTT                         GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT
genomic: AGTTCGGGGTGTGGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG
                                   tccttac  putative branch site (score: 2)
                                            ccttt  putative PPT
     tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcaccctttctttatctttgtctatttatttatttatttcctaggacttcaatttcttcttatttatttgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG