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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaataattgtaaggaaaaaagtctacttcaaatcttaaaatgtttcctaattatggatttgttgaaggaaaaaatcacactaagaatgctgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATG

Basic information

species Glycine max
transcript GLYMA01G29470.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 19
lower sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 18
gaaataattgtaaggaaaaaagtctacttcaaatcttaaaatgtttcctaattatggatttgttgaaggaaaaaatcacactaagaatgctgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATG-
         ||| ||||  || | || ||  | |||| | |    |  ||||| |   ||||| | |  | ||| | | | || ||| | || |  |||||| |||| |||||||||||||||||||||| ||||||| ||  | ||  |||| | ||| |    |||| |  |||               | ||  | | 
---------gtatggaatgaaatatattt--attcttcacacaagt--taatt-tctctttgtaggaaaacaaattaaaaatatgaa-gttgat--gcagATCTGGAAAGAGGAGATGCAACAGGTTTATCTGGGCAAGGCTGTTATCTCTGATGAAGTTGTTCCATAAAA-ACCACAATCAGAAATGGCAAGACGTAAGA

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 19
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 18
gaaataattgtaaggaaaaaagtctacttcaaatcttaaaatgtttcctaattatggatttgttgaaggaaaaaatcacactaagaatgctgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATG
         ||| ||||  || | || ||  | |||| | |    |  ||||| |   ||||| | |  | ||| | | | || ||| | || |  |||||| |||| |||||||||||||||||||||| ||||||| ||  | ||  |||| | ||| |    |||| |  |||               | ||     
---------gtatggaatgaaatatattt--attcttcacacaagt--taatt-tctctttgtaggaaaacaaattaaaaatatgaa-gttgat--gcagATCTGGAAAGAGGAGATGCAACAGGTTTATCTGGGCAAGGCTGTTATCTCTGATGAAGTTGTTCCATAAAA-ACCACAATCAGAAATGGCAAGAC-----

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 19
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 18
---gaaataattgtaaggaaaaaagtctacttcaaatcttaaaatgtttcctaatta-tggatttgttgaaggaaaaaatcacac-taagaatgctgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATG----
   ||  | | | |    ||     | ||| |   || |||     | |   ||  | ||||       ||| |  | |   ||  | | ||||   ||| |||||| ||||||||||| ||||| ||||||||| ||||||||  ||   | |||||||   | || ||||||  |||  ||  |||| |   ||| || | ||    
cttgaggtcactttcc--aattccttttacct--gattttatttcctgttgaaacaaatggagcctcaaaagaatgagaaagcatgtgataatgtcattt-gcagATCTGGAGAGAGGAAATGCAGCAGGTTTATCTGGGCAAATTCAAACTCCCTGAAGAGATTGAAAAATAATTTGCT-GGCTGCATGC---TCACACTCTTGGACA

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|22928940|gb|BU546079.1|BU546079
EST:     ACATTCAGAGAACAAACGTTCCTCACATCCGGTTGGAATTCCGTGATACG                         ATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCT
genomic: ACATTCAGAGAACAAACGTTCCTCACATCCGGTTGGAATTCCGTGATACGgtatggactt ... tgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCT
EST: gi|254332341|gb|GR846386.1|GR846386
EST:     ACATTCAGAGAACAAACGTTCCTCACATCCGGTTGGAATTCCGTGATACG                         ATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCT
genomic: ACATTCAGAGAACAAACGTTCCTCACATCCGGTTGGAATTCCGTGATACGgtatggactt ... tgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCT
EST: gi|26267857|gb|CA818920.1|CA818920
EST:     ACATTCAGAGAACAAACGTTCCTCACATCCGGTTGGAATTCCGTGATACG                         ATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCT
genomic: ACATTCAGAGAACAAACGTTCCTCACATCCGGTTGGAATTCCGTGATACGgtatggactt ... tgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctaattatggatttgttgaaggaaaaaatcacactaagaatgctgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATG
 tcctaat  putative branch site (score: 2)
                                            ctgtttt  putative PPT
                        aaaaaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaataattgtaaggaaaaaagtctacttcaaatcttaaaatgtttcctaattatggatttgttgaaggaaaaaatcacactaagaatgctgttttgcagATTTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - gaaaaaa
- - - - - - - - - - - -ctacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaatgc