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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgtctacttaaagcaatcatggaaaatataatgccttaattatattgggttcaaaaacaatacttattttctttatgttttctaatttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG

Basic information

species Glycine max
transcript GLYMA13G18660.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g56550.1 (Oryza sativa), 3'ss of exon 5
atatgtctacttaaagcaatcatggaaaatataatgccttaattatattgggttcaaaaacaatacttattttctttatgttttctaatttttt----tcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG
                            | |   |   ||  || |||    |         || ||| |  | |  ||    |  ||  |||       |||||||||||| |  || || ||||| |||||||| ||||||||| ||||  ||||||| ||| |  | |||||||| ||||| |||||| |||||| | |||
--------------------------gtacagtttttgttctttctatctcttctgtctgttatgcttctcat-tgcataacatggaaggtttcggcactgcagAGAGAAGCAACCATTGTCTATGCCACTCATATATTTGATGGATTGGAATCATGGGCTACTGACATTGCATACATCCAAGAAGGTGAATTGAGAAAATCAG

upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03905.1 (Arabidopsis thaliana), 3'ss of exon 5
---atatgtctacttaaagcaatcatggaaaatataatgccttaatta-tattgggttcaaaaacaatacttattttctttatgttttctaatttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG
     | || | | ||  | ||   |  ||   | |      |  ||| |  ||  ||     |  ||  ||   || |||||    |  |    ||  | ||||||| ||||| |||||| ||||||||||| || || || || || ||||||||||| || |||||||| ||||| || || ||||| ||||   |   | 
tgagcacgtattcgtattggaagattacaactcacacacttattcttactgatgacttattgcatgatctttgacttgtttataccattga----ttaactcagAGAGGAGCTACAATCGTGTATGCAACTCACATATTCGACGGGCTAGAGACATGGGCGACACATTTGGCCTACATTCAGGACGGTGAGCTGAATCGTTTAT

upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G44110.3 (Arabidopsis thaliana), 3'ss of exon 5
atatgtctacttaaagcaatcatggaaaatataatgccttaattatattgggttcaaaaacaatacttattt-tctttatgttttctaatttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG
                     | |  |   |  |  ||    | || ||  ||| | ||| |  |  |  |  | || ||||||| ||    |||  | |||||| ||||| ||| |||||||||||||||||||| || || || ||||||||||| | ||||||||| |||||  | |  || || |||| |    | |
-------------------gtaagccattcactaaccccccctcatcttatgtttagaaatatcaaatgctgattttcatgttttata----tttgagtagAGAGGAGCTACAATTGTATATGCAACTCATATTTTCGACGGGCTCGAGACATGGGCTAGTCATTTGGCTTACATTAATGGAGGAGAGCTGAAACTCTCGG

upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G44110.2 (Arabidopsis thaliana), 3'ss of exon 5
atatgtctacttaaagcaatcatggaaaatataatgccttaattatattgggttcaaaaacaatacttattt-tctttatgttttctaatttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG--
                     | |  |   |  |  ||    | || ||  ||| | ||| |  |  |  |  | || ||||||| ||    |||  | |||||| ||||| ||| |||||||||||||||||||| || || || ||||||||||| | ||||||||| |||||  | |  || || |||| |    | |  
-------------------gtaagccattcactaaccccccctcatcttatgtttagaaatatcaaatgctgattttcatgttttata----tttgagtagagAGGAGCTACAATTGTATATGCAACTCATATTTTCGACGGGCTCGAGACATGGGCTAGTCATTTGGCTTACATTAATGGAGGAGAGCTGAAACTCTCGGCC

upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------atatgtctacttaaagca----atcatggaaaatataatgccttaat---tatattgggttcaaaa--acaatactta--ttttctttatgttttcta-atttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG
                                          |   |   |||||||||    || || ||    | | | ||| ||    | | ||   || ||||  || ||| ||   ||||||||    | |  | || ||  |  ||| ||| ||||| ||| || |||||||| ||||||||||||||  ||||||||||||||||  || |||||||  | ||||| || ||  | || |     |
gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG

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|192305551|gb|FG994317.1|FG994317
EST:     TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
EST: gi|192305550|gb|FG994316.1|FG994316
EST:     TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
EST: gi|192309353|gb|FK000561.1|FK000561
EST:     TTGTTGCTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
EST: gi|58017128|gb|CX703870.1|CX703870
EST:     TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
EST: gi|22926919|gb|BU544058.1|BU544058
EST:     TTGTTACTNNGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAANNNTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
EST: gi|151394486|gb|EV264357.1|EV264357
EST:     TTGTTACTCAGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
EST: gi|151409900|gb|EV279708.1|EV279708
EST:     TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAG                         AGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA
genomic: TTGTTACTCGGATGGATTTATTGGACTTCTTTAAGGAAGAATGTGAACAGgtatttactg ... tttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgggttcaaaaacaatacttattttctttatgttttctaatttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG
                                     ttctaat  putative branch site (score: 2)
                        ttttctttatgttttc  CT-rich tract
          aaaaacaatacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgtctacttaaagcaatcatggaaaatataatgccttaattatattgggttcaaaaacaatacttattttctttatgttttctaatttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - -gcaatca
- - - - - - - - - - - -ggaaaata
- - - - - - - - - - - - - - - - aatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa