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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagcattttagcatgtacataattctgctgcataccatggaattgttgataatgacaaattatcaaatagcaatgatcaattctcaatcttgagt...

Basic information

species Glycine max
transcript GLYMA03G40860.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40860.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 5
GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagcattttagca-tgtacataattctgctgcataccatggaattgttgataatgacaaattatcaaatagcaatgatcaattctcaatcttgagt-----------------------------
 ||| | || ||||||||||||||||| ||||||||||| ||||| |||||||| || | ||||||    ||| | ||| || |  |       |||||||  || |||    || | ||| | |   |    |||  | |    ||||||  ||  | | |||      |    || |  || |||   ||||   |                             
AGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTGgtatcaagtattgacacagtctacctcagaatat--catttctttcttttgttgcaaaaaaaacatttcttggtctgcatca--aaatctttttcttagttcacttacagattttactttggcttgtcag

upper sequence: GLYMA03G40860.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagcattt-tagcatgtacataattctgctgcataccatggaattgtt-gataatgacaaattatcaaatagcaatgatcaattctcaatcttgagt-
||| |||||||||||||| || |||||||| || ||||| |||||||| ||||  ||||  | || ||| |||  ||| ||  || | ||     ||||| ||   ||||  |  ||    |||||| | || ||    |||  |||||| ||  |||     |       |    |  ||   || | ||    |  | 
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataatttt-ctaca-gtaatgttattgttagactatgttgtgtatgtgtgtgtggaacat-ggtttttaaaacggtatg

upper sequence: GLYMA03G40860.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagcattttagcatgtacataatt-ctgctg-cataccatggaattgttgataatgacaaattatcaaatagcaatgatcaattctcaatcttgagt---
||| ||||| |||||||| || |||||  |||||||||||||||| |||||||| || |  ||||||||||||| | ||||| ||      | | |||||||   ||||||  ||| |   |  || ||| |  | ||      |||   ||| |   | |  |  |||   | |||   |  ||||| |||  |   |   
GGAGCTTGGCATTGGAATAGTTCCATACTGTCCTCTTGGTCGTGGATTTTTTGGTGGTAGGGGAGTTGTGGAAAGTTTGCCTGCA------TACTTGgtata---cattttgtcattttttttgtttctgttttcttaatgcaaaatatctgaaagaaatat-tcttcaggaaacaa-agtatattctgaatgctccattta

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|254347025|gb|GR856695.1|GR856695
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACA
EST: gi|254327803|gb|GR834768.1|GR834768
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACA-GAACA-GAATATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
EST: gi|9259808|gb|BE347955.1|BE347955
EST:     TTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTTG                         AA-GCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATAT
genomic: TTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCT-Ggtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATAT
EST: gi|192325064|gb|FK016175.1|FK016175
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACA-GAACAAGAATATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
EST: gi|298186682|gb|HO037315.1|HO037315
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTGCAAATAGCTCCCTG                         AAAGCACATCCACGC
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGC
EST: gi|5753669|gb|AI960956.1|AI960956
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
EST: gi|254337008|gb|GR843187.1|GR843187
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACT
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACT
EST: gi|192305622|gb|FG994332.1|FG994332
EST:     TTTTTGGCGGCAAAG-AGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AA-GCACATCCACGCTTTCA-GCCGAGAACTTAGAC
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGAC
EST: gi|12774742|gb|BG239669.1|BG239669
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
EST: gi|254323788|gb|GR836127.1|GR836127
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCA-GCCGAGAACTTAGACA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACA
EST: gi|254347733|gb|GR853982.1|GR853982
EST:     TTTTTGGCGACAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACA-GAACAAGAATATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
EST: gi|151394300|gb|EV264171.1|EV264171
EST:     CTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCA-GCCGAGAACTTA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTA
EST: gi|14011842|gb|BG726764.1|BG726764
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCG
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCG
EST: gi|254332024|gb|GR846227.1|GR846227
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACAATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACA-GAATAT
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACA-TCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATAT
EST: gi|192306323|gb|FG995103.1|FG995103
EST:     TTTT-GGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGA-CTTAGACA-GA-CA-GA-TATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
EST: gi|192301004|gb|FG990104.1|FG990104
EST:     TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG                         AAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA
genomic: TTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagca ... caattatcagAAAGCACATCCACGCTTTCAAGCCGAGAACTTAGACAAGAACAAGAATATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagcattttagcatgtacataattctgctgcataccatggaattgttgataatgacaaattatcaaatagcaatgatcaattctcaatcttgagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG