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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggattttttattcaattatcaatttcatgaagcttctcatgttcacaacttgctaggatatagttatgatatatttttccacaaaaaatttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT

Basic information

species Glycine max
transcript GLYMA06G42840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------------------gtggattt--tttattcaattatcaatttcatgaagcttctcatgttca---caacttgctaggatatagttatgatatatttttcca----caaaaaattta-tatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT
                                                                 | || |  || | | |  || ||  |   ||    || |    || |   | |   ||  |      ||| || ||    |||  |         |||| | ||| ||||||| |||||| ||||||| ||||| || || || ||||| ||||| ||||||||||| || ||||| || || || || ||| | || || ||||| |
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 6
gtggattttttattcaattatcaatttcatgaagcttctcatgttcacaacttgc-taggatatagttatgatatatt----tttccacaaaaaatttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT
     | ||| |    ||||         |     |||     |    || ||   | |  |    || || |  |      |||   |    |      ||||||||||||||||| ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||||||| | || |||||||| |
-----tatttcagaacattaatgccgcagtatgttttcctgcatgtttaatttatgtggtgttctattttgtttcaccatgatttttgctctcatcgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCCCCAGAACTTATATTTGGTGCAACTGAATACACAACATCGATTGATATTT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 7
gtggattttttattcaattatcaatttcatgaagcttctcatgttcacaacttgctaggatatagttatgatatatttttccacaaaaaatttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT
                 |      || ||   ||  ||    |    || |  |||  ||| |   | |  |   ||| |   ||||| |     | ||||| || || ||  | ||||| || || || ||||| ||||| || || ||||| ||||| ||||||||||||||||| |||||| |  | || || ||||
----------------gtgggtgcttacaaataggatccttggaattcagca-gct--gatttgcgtttcctgcttttcttggcaaaaca-----aacagGTGAAAGGAGAGCCCAACATATCGTATATCTGTTCCCGTTATTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

upper sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 7
gtggattttttattcaattatcaatttcatgaagcttctcatgttcacaacttgctaggatatagttatgatatatttttccacaaaaaatttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT
                 |      || ||   ||  ||      |   || |    ||   ||     |    |  ||||||    |||    | | ||||| ||||| ||  | ||||| || || || ||||| |||||||| || ||||| ||||| ||||||||||||||||| |||||| |  | || || ||||
----------------gtgggtgcttacaaataggatc-----cttggaattcagcagctgatttgcgtttcctgcttttcctggcaaa----acaacagGTGAAGGGAGAGCCCAACATATCGTATATCTGTTCCCGTTACTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

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|193500521|gb|FK464052.1|FK464052
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|193656739|gb|FK603771.1|FK603771
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|193328173|gb|FK293410.1|FK293410
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCGAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|17023095|gb|BM094129.1|BM094129
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|11689096|gb|BF596772.1|BF596772
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCC
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGG-C
EST: gi|193403386|gb|FK367708.1|FK367708
EST:     TTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCGAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: -TCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|6502169|gb|AW203542.1|AW203542
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|9819612|gb|BE555125.1|BE555125
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|193432041|gb|FK393839.1|FK393839
EST:     AAGCTATGTGTTATTTTTGGGTAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: AAGCTATGTG--A-TTTTGGG-AGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|208124192|gb|GD922000.1|GD922000
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
EST: gi|207763538|gb|GD736653.1|GD736653
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGT
EST: gi|42723166|gb|CK769065.1|CK769065
EST:     CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTG                         GTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT
genomic: CTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAAGTTCTGgtatgttggt ... tttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaacttgctaggatatagttatgatatatttttccacaaaaaatttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT
              atatagttatgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggattttttattcaattatcaatttcatgaagcttctcatgttcacaacttgctaggatatagttatgatatatttttccacaaaaaatttatatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT

- - - - - - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - cttgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaa