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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGCTGCGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatttgtaaacccgctcttttaaatttttcattttttccatgttagttttattttctctgtgtctgtgtggttggttataaatttcaggctcagttacttacagttttcttcattttgtag

Basic information

species Glycine max
transcript GLYMA20G22600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22600.3 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 2
---GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGCTGCGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatttgtaaacccgctcttttaaatttttcattttttccatgttagttttattttctctgtgtctgtgtggttggttataaatttcaggctcagttacttacagtt-ttcttcattttgtag
    ||||| || || |||||||||||| | ||||| ||    || |  | |   ||||| |||||||| |||||||| || ||||||||||||||||| | ||||||| |         |   |  ||    || ||| | ||     ||||  || | ||||  |||    |   || ||  | || | || ||   |  |||||| |      ||||| |||||  ||
CATAGCACCTACCTCTGGTTTGAGAGAACCTAGTGGCCACAATGCCGGTGTT---GATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttac---tgttccttgtcttttgcctgcacttaattgattattgatcatttgca---ttggttactgaagacagttcttgatttttcag
















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|213589828|gb|DB969621.1|DB969621
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|26058927|gb|CA801841.1|CA801841
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|209720625|gb|BW654452.1|BW654452
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|193375822|gb|FK343069.1|FK343069
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAAGACAGGACATAT
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGA-GACAGGACATAT
EST: gi|193633458|gb|FK584654.1|FK584654
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAAC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAAC
EST: gi|209699787|gb|BW655800.1|BW655800
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|18039891|gb|BM308185.1|BM308185
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|192296530|gb|FG991636.1|FG991636
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|22522553|gb|BU081364.1|BU081364
EST:     ATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: ATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|213616715|gb|DB971240.1|DB971240
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|208056113|gb|GD850740.1|GD850740
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|15814184|gb|BI786459.1|BI786459
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGTTGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|254333709|gb|GR848627.1|GR848627
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|254327042|gb|GR836651.1|GR836651
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGACAGGACATATC
EST: gi|193335410|gb|FK299368.1|FK299368
EST:     CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGAACAGGACATAT
genomic: CGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAACGGAACGGAGA-CAGGACATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGCTGCGGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatttgtaaacccgctcttttaaatttttcattttttccatgttagttttattttctctgtgtctgtgtggttggttataaatttcaggctcagttacttacagttttcttcattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG