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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTGCTGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTGCCCATGGAAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtcagtggtttttcttgtcatgtgtactgttaactacattctatactgataatttcctttcggggtttctatcttccag

Basic information

species Glycine max
transcript GLYMA11G34840.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 7
GGATGGTGCTGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTGCCCATGGAAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgta-----cgctgtcagtggtttttcttgtcatgtgtactgttaactacattctatactgataatt-tcctttcggggtttctatcttccag---------
|||   |||||| ||||| || || || || || || |||||||| || || || |||||| | ||  |||||||||| ||||||||||||||||||||||||      |||   | | ||||||||| || |  | ||| || | || | |    || | | | | |   |      |   |||    |           
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttctt-tctttagaactatttaatataataggcacagttgactgttactgaacaatacttattagacttaaccaaata

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 8
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 5'ss of exon 7
GGATGGTGCTGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTGCCCATGGAAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgt--acgctgtcagtggtttttcttg-tcatgtgtactgttaactacattcta--tactgataatttcctttcggggtttctatcttccag
||||   || |||||||| ||||| ||||| ||||||||||| ||||| ||||| |||||||| || || || || |||||||| || |||||||| |||||  | ||   || |  | | | ||  |||| |  | |  |    | |   ||  |  ||| | ||   || |    | | |  |   |||
GGATAACGCAGGGTTTCCTGCTGTGGTAACGGCTCATTTTGTACCCATTGAAGGACAACAACGTCCTCGAACTACTATTTTGATCAAGTTTGCTGATGAGgttaatgcctacattcatctcttttcctcatctagatttgtgggaaaaacttaattcttgacagttgttttac---ttctatgccgcacag

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 7
GGATGGTGCTGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTGCCCATGGAAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtcagtggtttttct-tgtcatgtgtactgttaactacat-tctatactgataatttcctttcggggtttctatcttccag------------
|||| |||| || ||||||||||| ||||||||||| ||||| || ||||| |||||||||||||| |||||||| |||||||| ||||||||||||||||||  |      |     || | ||| |  || ||  || |  |||  || | |   |  |    | | |       || |    |              
GGATAGTGCAGGTTTTCCAGCTGTGGTAACAGCTCACTTTGTACCTATGGAGGGTCAACAACGACCTCGGACAACTATTTTGATTAAATTTGCTGAAGAGgtaaacatatgttatcccttttctgttacttgcacatttgatcacagatccacatgaactaaacacctccaaaccaccttttcctcttttcctttggtta

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|208195299|gb|GD990878.1|GD990878
EST:     CAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: CAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|254320117|gb|GR831033.1|GR831033
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|151411948|gb|EV281759.1|EV281759
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|193593981|gb|FK546223.1|FK546223
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|151396616|gb|EV266493.1|EV266493
EST:     AGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTC
genomic: AGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAA-GAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTC
EST: gi|192320522|gb|FK011932.1|FK011932
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|208340390|gb|GE137044.1|GE137044
EST:     AAAATTTGCTGAAGAG                         GNGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|193728284|gb|FK665054.1|FK665054
EST:     GTTCTAACTAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: G-TC-AAC-AACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|151405191|gb|EV275005.1|EV275005
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGACTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|208300303|gb|GE097632.1|GE097632
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATGCCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|193563080|gb|FK519513.1|FK519513
EST:     AAGGTCAACAACGACCGCGGACAACA-TTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAG
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAG
EST: gi|193624022|gb|FK572992.1|FK572992
EST:     GACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAACAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: GACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|192320523|gb|FK011933.1|FK011933
EST:     AAAGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGA
EST: gi|151412057|gb|EV281869.1|EV281869
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGA
EST: gi|42723157|gb|CK769056.1|CK769056
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|193385026|gb|FK351942.1|FK351942
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|6746980|gb|AW317436.1|AW317436
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|208061577|gb|GD860481.1|GD860481
EST:     CAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
genomic: CAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA
EST: gi|9987096|gb|BE661204.1|BE661204
EST:     AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAG                         GTGTTACAAAGAGAAGCAAGAT-AGGCTGATGTTTATACCAAGAATTT-CA
genomic: AAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtc ... tatcttccagGTGTTACAAAGAGAAGCAAGATTAGGCTGATGTTTATACCAAGAATTTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGTGCTGGGTTTCCAGCTGTTGTAACAGCTCATTTTGTGCCCATGGAAGGTCAACAACGACCGCGGACAACAATTTTGATAAAATTTGCTGAAGAGgtacgctgtcagtggtttttcttgtcatgtgtactgttaactacattctatactgataatttcctttcggggtttctatcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA