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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtaagggaatatgacatttatgaatggttggcaatgtttgtaattgcttctgatgcaacttgtcctcaaagaataaccgcgtaagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAG

Basic information

species Glycine max
transcript GLYMA10G35560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 2
tagtaagggaatatgacatttatgaatggttggcaatgtttgtaattgcttctgatgc--aacttgtcctcaaagaataaccg----cgtaagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAG
           | ||   ||     |||       |||  | |   |   | |  |||  ||||  ||||  ||   | || |     | |  ||  | | || ||  | || ||||| ||  |||||||||| || |||||||||||||||||||| |||||  | |||||      ||| |
------atttctttggtgttcgctgatgccaaaggatgaattttcctcgatgtattgctaaactattcctgtaatgtttactgattctgaagattgatttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG

upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 2
tagtaagggaatatgacatttatgaatggttggcaatgtttgtaattgcttctgatgcaacttgtcctcaaagaataaccgcgtaagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAG
                          |  || |        | ||   |||   ||  ||  | |  ||     ||   |  ||  |||    |   ||||||||| ||||||||| | || |||||||||||||| ||||||||||| ||    ||||  || ||||| |||||||
-------------------------gtattttgaggaagaagaaagctcttactatataa--tatgatcgtttgatttacatgttggtttgctttattagGAGGCCTGGTCAGAGCAGGATCACAACTCCTAGAAAAGAGACTGATACTTGCCGGATATCGTCTGGAGTCTCTGAAG

upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 2
tagtaagggaatatgacatttatgaatggttggcaatgt-ttgtaattgcttctgatgcaacttgtcctcaaagaataaccgcgtaagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAG
|||||  |    |  | | || | | || |   || ||  || | ||| |||||||||  |  | || | || |  | ||        || || ||| ||||||||||||||||||||||||||| || || || || ||||||||||| ||   ||||| ||| |||||| ||||||
tagtattgtt-cacaaaaattttcactgatgaacactggattctgatttcttctgatgtcaaatttcttgaagggtttacatttatttttgttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG

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|26058445|gb|CA801359.1|CA801359
EST:     CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|193387927|gb|FK355178.1|FK355178
EST:     CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAG
genomic: CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAG
EST: gi|193690154|gb|FK634535.1|FK634535
EST:     GAAGCTGATATGCAATTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: GAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|37996069|gb|CF807658.1|CF807658
EST:     CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|19453140|gb|BM954550.1|BM954550
EST:     CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|6666177|gb|AW277636.1|AW277636
EST:     CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttctgatgcaacttgtcctcaaagaataaccgcgtaagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAG
                           gaataac  putative branch site (score: 2)
                                          ttcttat  putative PPT
                        aaagaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtaagggaatatgacatttatgaatggttggcaatgtttgtaattgcttctgatgcaacttgtcctcaaagaataaccgcgtaagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG