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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatttatttcttctaattaagatttatttcactttgacttactttgcgagtcatatcttaaatatcttatttcattgtctgtgacttcgtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGAAGATGTTGCAGAAGACTAGATAGTGATAAAAGCTGCTAATGGCTATGAC

Basic information

species Glycine max
transcript GLYMA20G21250.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G21250.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 4
ataatttatttcttctaat-taagatttatttcactttgacttactttgcgagtcatatcttaaatatc-ttatttcattgtctgtgacttcgtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGAAGATGTTGCAGAAGACTAGATAGTGATAAAAGCTGCTAATGGCTATGAC-
  |||  ||       ||| |       | || |  ||  ||||  |        || | | |||      |   || |  | ||     |    | |  |||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| | ||    |||||||  |  ||||  ||| |    |   | | |  
-gaatccataaacctcaatgtgcagaagagtttatgttt-cttatgtgaatttcaatgtgtaaaaagctactgaatcttcttttgatgtatttcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGAAGAAGCTGACCGAGACTAGG-ATGGATATCAGCAGTGGTTTAGTGTAATC
















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|192295086|gb|FG986805.1|FG986805
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|58022880|gb|CX709621.1|CX709621
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|10234556|gb|BE803444.1|BE803444
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|12689942|gb|BG156278.1|BG156278
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|58020838|gb|CX707580.1|CX707580
EST:     GAGTACATTGAGGTACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|14990237|gb|BI315910.1|BI315910
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|7588010|gb|AW703815.1|AW703815
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGGAGTA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGG-AGTA
EST: gi|151400274|gb|EV270088.1|EV270088
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|17964468|gb|BM271203.1|BM271203
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|5677258|gb|AI938388.1|AI938388
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|31464033|gb|CD406061.1|CD406061
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|192308445|gb|FK002817.1|FK002817
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAAGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|31312516|gb|CD397719.1|CD397719
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|21600407|gb|BQ610738.1|BQ610738
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|254325850|gb|GR838731.1|GR838731
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|192327100|gb|FK015492.1|FK015492
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|18692955|gb|BM521803.1|BM521803
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|254324568|gb|GR833993.1|GR833993
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|31469700|gb|CD411728.1|CD411728
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|208150579|gb|GD945108.1|GD945108
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGAATAGAAGGAAAT
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGA-T-GA-GGAAAT
EST: gi|192310362|gb|FK002242.1|FK002242
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAACGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|192323685|gb|FK015991.1|FK015991
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|31473931|gb|CD415959.1|CD415959
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|151399653|gb|EV269524.1|EV269524
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|18848468|gb|BM567685.1|BM567685
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
EST: gi|192324854|gb|FK016070.1|FK016070
EST:     GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAG                         ATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA
genomic: GAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattcca ... gtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgagtcatatcttaaatatcttatttcattgtctgtgacttcgtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGAAGATGTTGCAGAAGACTAGATAGTGATAAAAGCTGCTAATGGCTATGAC
                                              tatttct  CT-rich tract
         atatcttaaatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatttatttcttctaattaagatttatttcactttgacttactttgcgagtcatatcttaaatatcttatttcattgtctgtgacttcgtatttctagATGTAACAATGTTCTCTACCTTCGAGGAGTACCGGAGGATGAGGAAATCGAAGATGTTGCAGAAGACTAGATAGTGATAAAAGCTGCTAATGGCTATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgtg