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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCAGCGAAGTATTTGTACATCAACTTATACATACCATAGAATTTGTACTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctataagtcccagacgttctattctaatagtaattcttgagtcccactagaaacaaggttgaaaccttacatcatgcagtttattacttttgtttatctattcgtctatagatatgtttgatgcatgtattgaactgctttacgcatttactgatgttttccttttctgtacccag

Basic information

species Glycine max
transcript GLYMA12G04330.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04330.1 (Glycine max), 5'ss of exon 16
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTTCAGCGAAGTATTTGTACATCAACTTATACATACCATAGAATTTGTACTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtcta-taagtcccagacgttctattctaatagtaattcttgagtcccactagaaacaaggttgaaaccttacatcatgcagtttattacttttgtttatctattcgtctatagatatgtttgatgcatgtattgaactgctttacgcatttactgatgttttccttttctgtacccag
| ||||||||  ||||||| ||||| || || || |||||||| ||||| || ||||| || || || || ||||||||||| ||||||||||| || |||||||  || ||    | | || |   |||  |  |   || || | | |  | ||   |     |||   |                                                                                                               
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatga-attacataacctatactcgtggcttaatatccattcttttgtttcag-------------------------------------------------------------------------------------------------------------

upper sequence: GLYMA12G04330.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 5'ss of exon 16
AGTTCAGCGAAGTATTTGTACATCAACTTATACATACCATAGAATTTGTACTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctataagtcccagacgttctattctaatagtaattcttgagtcccactagaaacaaggttgaaac-cttacatcatgcagtttattacttt-tgtttatctattcgtctatagatatgtttgatgcatgtattgaactgctttacgcatttactgatgttttccttttctgtacccag
| ||| | ||||| ||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| || || ||||| ||  |||||||||| |||||  |   ||       ||  |||| ||| | | || ||| |   ||   | || | | |    || | | |  | |  ||  |   |   | ||| ||||                                                                                  
AATTCGGTGAAGTTTTTGTACATCAACTTATACATACGATTGAATTTGTACTTGGAGCAGTCTCCAATACCGCATCATACCTTCGATTATGGGCCCTCAGgtacatagctagaaatttgaatttctgttccatt-gtgattgtgaggttata-tatatatatatatgtatctcccataatatatatcctgagattttatgtt----------------------------------------------------------------------------------
















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|58015179|gb|CX701921.1|CX701921
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|209710485|gb|BW662021.1|BW662021
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|151394145|gb|EV264016.1|EV264016
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|58017582|gb|CX704324.1|CX704324
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|192300278|gb|FG988785.1|FG988785
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATG
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATG
EST: gi|254334718|gb|GR844503.1|GR844503
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|193549546|gb|FK510587.1|FK510587
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|58021456|gb|CX708197.1|CX708197
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
EST: gi|105633551|gb|DW246914.1|DW246914
EST:     CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAG                         TCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT
genomic: CTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctat ... ctgtacccagTCTCGCTCATTCAGAGTTATCAAGTGTATTCTATGAGAAGGTTCTGATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCAGCGAAGTATTTGTACATCAACTTATACATACCATAGAATTTGTACTAGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctataagtcccagacgttctattctaatagtaattcttgagtcccactagaaacaaggttgaaaccttacatcatgcagtttattacttttgtttatctattcgtctatagatatgtttgatgcatgtattgaactgctttacgcatttactgatgttttccttttctgtacccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG