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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA

Basic information

species Glycine max
transcript GLYMA17G37820.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 10
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-
          ||  |   ||  |||| ||  | ||  | |   |||     |||   | | || |||     ||   ||  |  |   ||      ||||||| || || || ||||||||||| || |||||||| ||||||||||| || |||||||| || || ||||| |||||||||||||| ||  | ||| 
----------gtactagattactatttca--tgaacgacacggtattccattcat--tgacttatgcagcctaaaccta--taagctattatctgtagGGTCTCGTCGACTCGGACACATTGCCTCTCAATGTATCACGAGAAATGCTCCAACAACATAGCAGCCTGAAGACCATCAAGAAGAAACTAATCCGCAAAG

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-
          ||  |   ||| || | ||     || ||||   || |   | | |   || | |  || ||||| ||||  | ||  ||      ||||| ||||||| || |||||| |||| || ||||| || ||||||||||| || |||||||| ||||| ||||| ||||||||||| || ||  | ||| 
----------gtactatattgctacttcaagagcaa-atatacaattaatttgaaaggcatatgttatactaaatcttacagt-gatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataattt--ttgctaa-taaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-
          ||  ||  ||  | || ||   ||    || | |   ||  |||   | || |  | ||    ||||  ||||  | |   ||      ||||| ||||||| || |||||  |||| || || || || |||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||  | ||| 
----------gtactgtattactgtttcaagaaacgcgtactattcaat--tcaatctgatgtcatagcaggctaaaccttacagt-ggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 10
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-
             ||    |  | |   ||| ||| ||     |    | |  | ||   | |  ||||| |    | || |  |  | |     |||||||||||||| |||||||||||||| || ||||||||  ||||||||||||| ||||| || ||  |||||||||| |||||||| |||||  | ||  
-------------gtaaactact-tgaaagacaaactaaggggttctttcaatacaaatttatgggctaa-atccctaacgtgagttgcttttg-cagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTTCAACAACACAGCAGCTTAAAGACAATTAAGAAGAAGCTTATCCGAAAGG

upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
ggtaggaattg--ttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttt-tgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-
| ||  |||    || |   ||  |||||  | |    || | |  |  ||  |  |||| |  |||   | | | | | | |   |||||||  || ||||||||||| ||||| ||||| || || |||||||| || |||||||||||||| ||||| || ||| | || ||||| |||||||| |||||  | ||  
gttataaatcaatttataaattcctattg-ggttcttgtaaactggagaatt-tatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG

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|207691791|gb|GD674360.1|GD674360
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|58017096|gb|CX703838.1|CX703838
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|207788143|gb|GD760205.1|GD760205
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|208206790|gb|GE004639.1|GE004639
EST:     TTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: TTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|10848102|gb|BF071680.1|BF071680
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|193473475|gb|FK438772.1|FK438772
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|208324095|gb|GE121392.1|GE121392
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTGAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
EST: gi|193353431|gb|FK323637.1|FK323637
EST:     ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCT                         GGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT
genomic: ATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaatt ... gttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA
             aataatttttgctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA