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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgccagtaagggaatatgacatttatgaatgatcggtaatgtttgcttctgatgcaacttgtcttcaaagattaactgcataagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAG

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 2
aactgccagtaagggaatatgacatttatgaatgatcggtaatgtttgcttctgatgcaacttgtcttcaaagatta---actgcataagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAG
   |  |  |   |     |||     | | ||||    |  |   ||  | || |  |   |  ||  || | |||   | |    |  ||  | | || ||  | || ||||| ||  |||||||||| || |||||||||||||||||||| |||||  | |||||       || |
--atttctttggtgttcgctgatgccaaaggatgaattttcctcgatgtat-tgctaaactattcctgtaatgtttactgattctgaagattgatttatacagACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 2
aactgccagtaagggaatatgacatttatgaatgatcggtaatgtttgcttctgatgcaacttgtcttcaaagattaactgcataagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAG
                        | | |  | ||     || | |  |||   ||  ||  ||          |||  ||  |   ||  | | | ||||||||| ||||||||| | || |||||||||||||| ||||||||||| ||    ||||  || ||||| || ||||
-----------------------gtattttgaggaagaagaaagct--cttactatataatatgatcgtttgatttacatgt-tggtttgctttat-tagGAGGCCTGGTCAGAGCAGGATCACAACTCCTAGAAAAGAGACTGATACTTGCCGGATATCGTCTGGAGTCTCTGAAG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 2
aactgccagtaagggaatatgacatttatgaatgatcggtaatgtttgcttctgatgcaacttgtcttcaaagattaactgcataagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAG
 | |     | |   ||  |  || | |||||   | | |  || || |||||||||  |  | |||| || | || ||        || || ||| ||||||||||||||||||||||||||| || || || || ||||||||||| ||   ||||| ||| |||||| | ||||
tagtattgttcacaaaaattttcactgatgaacactggattctgatttcttctgatgtcaaatttcttgaagggtttacatttatttttgttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG

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|37994824|gb|CF806413.1|CF806413
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|209717805|gb|BW668942.1|BW668942
EST:     CCTCGCCTTCCCCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|14125803|gb|BG790241.1|BG790241
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTGGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|254322919|gb|GR835634.1|GR835634
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|37996436|gb|CF808025.1|CF808025
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|254316986|gb|GR828523.1|GR828523
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|192325343|gb|FK017144.1|FK017144
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|298181206|gb|HO022645.1|HO022645
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|192296954|gb|FG991950.1|FG991950
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|254340228|gb|GR858353.1|GR858353
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGAC---A-                         GA----AGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|7692116|gb|AW760231.1|AW760231
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAAGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|209706545|gb|BW667810.1|BW667810
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|213594292|gb|DB969970.1|DB969970
EST:     CCTCGCATTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
EST: gi|21286048|gb|BQ473919.1|BQ473919
EST:     CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAG                         GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG
genomic: CCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttgcct ... ttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttctgatgcaacttgtcttcaaagattaactgcataagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAG
                           gattaac  putative branch site (score: 2)
                                          ttcttat  putative PPT
                        aaagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgccagtaagggaatatgacatttatgaatgatcggtaatgtttgcttctgatgcaacttgtcttcaaagattaactgcataagttcttatgtatagGAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
-actgcca
- - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa