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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatatcccaatttaccctattttaccatgataaaatgctttggtagcacaacactgtttacattgtgacctctgtttggaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAACGTTCGTGTTGCAAAGCTCTTGGGAGGGGGCTTGCATAACAGTACTGTAG

Basic information

species Glycine max
transcript GLYMA02G07910.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 3
----gtgagtatatcccaatttaccctattttaccatgataaaatgctttggtagcacaacactgtttacattgtgacctctgtttggaaaatat--agGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAACGTTCGTGTTGCAAAGCTCTTGGGAGGGGGCTTGCATAACAGTACTGTAG
    |  | || || |||  ||||   |    ||  || |    | |      | ||  | |||| |  ||   | |     | ||| ||  | |  |||| ||||| ||||| ||||||||||| ||||||||||||||||| ||||| ||| | || || |||||  | ||||| || ||||| ||   | |||| |
gtaagataatacataccagcttac---agggaactttgcttttttccccacaca-catcatactgatatcagc-taatagtgggttgtaacttttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCTGCAAACTTTAATGTTGACAATGTTAGAGTGGCTAAGCTACTTGGAGGTGGTTTGCACAATTCTTCTGTGG

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 3
----------gtgagtatatcccaatttacccta--ttttaccatgataaaatgctttggtagcacaacactgtttacattgtgacctctgtttggaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAACGTTCGTGTTGCAAAGCTCTTGGGAGGGGGCTTGCATAACAGTACTGTAG
             | || |    ||   |||  |  |||||   |    || |  || | |   || |      | | |||| |     ||  | ||   | ||||| ||||| ||||| ||||||||||| || |||||||| ||||| ||||| ||| | || || |||||  | ||||| || ||||| ||   | |||| |
gttctcaaatcaaactaaaaaggaaaaaaccgaaggttttatgttatgtaattatttagatgatacca----actaatattgggtttgttgcatcgatttt-tagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAATGTTAGAGTGGCTAAGCTGCTTGGAGGTGGTTTGCACAATTCTTCTGTGG
















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|192299740|gb|FG987785.1|FG987785
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCAAAA-CCCTGCAAACTTTAATGTGGACAAC
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
EST: gi|209700023|gb|BW656204.1|BW656204
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
EST: gi|16997151|gb|BM086523.1|BM086523
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
EST: gi|209728113|gb|BW655348.1|BW655348
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCCAAAAACCCTGCAAACTT
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCC-AAAAACCCTGCAAACTT
EST: gi|193548048|gb|FK505217.1|FK505217
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
EST: gi|26045600|gb|CA783137.1|CA783137
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
EST: gi|298187418|gb|HO034567.1|HO034567
EST:     CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGAT                         GCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC
genomic: CCAGCAAGCAATTTGGTCAAGAAGATATCATATGTTCGCTTGTTGCTGATgtgagtatat ... gaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgctttggtagcacaacactgtttacattgtgacctctgtttggaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAACGTTCGTGTTGCAAAGCTCTTGGGAGGGGGCTTGCATAACAGTACTGTAG
                                              aaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatatcccaatttaccctattttaccatgataaaatgctttggtagcacaacactgtttacattgtgacctctgtttggaaaatatagGCATGCATCCAAGTGTGCCCCAAAAACCCTGCAAACTTTAATGTGGACAACGTTCGTGTTGCAAAGCTCTTGGGAGGGGGCTTGCATAACAGTACTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG