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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttaagacagcaaatacataaaaaagctgtctaaaacattagaaattcttcctttatatcttttcttcctgacagactaattcttttatatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA

Basic information

species Glycine max
transcript GLYMA16G17370.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17370.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G145280_T01 (Zea mays), 3'ss of exon 3
aagttaagacagcaaatacataaaaaagctgtctaaaacattagaaattcttcc-----tttatatcttttcttcctgacagactaattcttttatatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA
   ||  |     |      |  ||      ||| |    | | |  ||    |     | | | |  | ||||  ||  | |  | ||  | | |  ||   ||||||| || || || ||||| ||||||||||| ||||| |||||||||||||||||| | |||||    ||  | ||| | |||||||||||||| ||||
---ttctgcatttatccttgttgaattatcttcttatgagtcacacttttcatcgatgatctgtgttatatcttgatgctaaa--agttactatgttgattgcagGCTGCTGGCATCCCAAAGAAGCTTGCTCCAACCATTGGTATTTCTGTTGATCACCGCCGCAAGAACAAATCCCTTGAGGGACTGCAGGCCAATGTCCAGA

upper sequence: GLYMA16G17370.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
aagttaagacagcaaatacataaaaaagctgtctaaaacattagaaattcttcctttatatcttttc---------ttcctgacagactaattctttta--tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA
                |  ||     |  | |  ||     ||    ||||  |||||||  | ||           || |    |  |  |||||||   | | |  |||| ||| || || || |||||  | |||||||| || || |||||||||||||||||  | ||||| |||||||||||| |||| ||| ||||||| || |
-------------gtttggattcttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA

upper sequence: GLYMA16G17370.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S58_38V6.1 (Physcomitrella patens), 3'ss of exon 3
aagttaagacagcaaatacataaaaaagctgtctaaaacattagaaattcttcctttatatcttt---tcttcctgacagactaattcttttatatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA
    | |   |     |  |        |  |       |  |  | || |   ||| | | | |   |  | ||||| ||| |     || |  | | ||||||||| || || || ||||| |||||||| |||||||| ||| ||||||| || ||| | |||||||| | |||||||||||| ||||  ||  |  |  
--catgatgaacttggtgtagggttccacctttcttggtacgatgatttatggttttttttgtctgggttgttctgac-gacaatcaaattgaattttactagGCTGCTGGCATCCCGAAGAAGCTTGCTCCCACTATTGGTATTGCTGTTGACCATCGCCGCAAGAATCGATGTTTGGAGAGTCTTCAGGAGAACATCAATC

upper sequence: GLYMA16G17370.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S459_9V6.3 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------aagttaagaca-gcaaatacataa--aaaagctgtctaaaacat-tagaaattcttcctttatatct--tttcttcctg----acagactaattcttttatat--atcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA
                                                                       ||||  ||   |||  |||||     |||||  |     |||  || |     |      || |||  || |   | |    |  ||||||| ||| | | |   ||  ||||||| ||||| |||||||||||||| || || ||||| ||| ||||||||||| |  | ||||| || |  |||||||| || ||||  |||||| |  
gtatgaattcctttgacctcagtataggattttatcattgacaccacttctgtttggttgcgcaatggattagttgtgatttgcacttacatggcggaaagccattagttacagataaagggcttgaacgaatgtctggttccactccggtgcatggactaatacttctttgttggtctcagGCTGCTGGAATCCCCAAGAAACTTGCCCCTACAATTGGTATTGCTGTTGATCACAGACGCAAGAACCGATGCTTGGAGAGCCTTCAGGAGAATGTGAACC

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|208054633|gb|GD850612.1|GD850612
EST:     GCCGGGAGAGGATTTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAGCTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: GCCGGGAGAGGA-TTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|254339157|gb|GR847874.1|GR847874
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|209719490|gb|BW650995.1|BW650995
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|193366313|gb|FK333688.1|FK333688
EST:     GGGAGAGGATTTTCACCGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: GGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|20207618|gb|BQ133707.1|BQ133707
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|16348456|gb|BI974051.1|BI974051
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|208110520|gb|GD913124.1|GD913124
EST:     AAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: AAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|120529623|gb|EH257757.1|EH257757
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|23726992|gb|BU761509.1|BU761509
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|6915365|gb|AW396895.1|AW396895
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|208069895|gb|GD867940.1|GD867940
EST:     GCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: GCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|213594019|gb|DB961935.1|DB961935
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|9204549|gb|BE330773.1|BE330773
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|193562396|gb|FK518185.1|FK518185
EST:     GCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACCATTGGGATTTCTGTTGAT
genomic: GCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|193567522|gb|FK524237.1|FK524237
EST:     AGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: AGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|18040171|gb|BM308465.1|BM308465
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|12688119|gb|BG154455.1|BG154455
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|208081632|gb|GD882060.1|GD882060
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|208175833|gb|GD977242.1|GD977242
EST:     CAACATAG-AAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: CAACAT-GAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|208135724|gb|GD936681.1|GD936681
EST:     AGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: AGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|26047262|gb|CA784114.1|CA784114
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|151402405|gb|EV272218.1|EV272218
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
EST: gi|17400476|gb|BM177258.1|BM177258
EST:     ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAG                         GCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT
genomic: ACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgac ... tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcttcctttatatcttttcttcctgacagactaattcttttatatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA
                               gactaat  putative branch site (score: 2)
                                     ttcttttat  CT-rich tract
                                actaattcttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagttaagacagcaaatacataaaaaagctgtctaaaacattagaaattcttcctttatatcttttcttcctgacagactaattcttttatatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG