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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatttggttagagctttttctgatatttttttgttccttataatattgaataactgatactaagttgcatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTTGATCGCCCACTTGAACCGTATGTGATGCCTCCTAGAAGCGTACGGGAAA

Basic information

species Glycine max
transcript GLYMA19G36450.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
ttcatttggttagagctttttctgatatttttttgttccttataatattgaa-taactg-atactaagttgcatttactt-----gcat-tattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTTGATCGCCCACTTGAACCGTATGTGATGCCTCCTAGAAGCGTACGGGAAA
           |  |  | || |  ||   || |  || |   | | || || || ||  |||  | | ||   || |||     |||| || ||||  ||   | ||||||||||||| ||||| ||||| ||| |||| | ||||||||| ||   ||||||||| |||||||| | ||||||||| ||  |    || | ||| |
-------caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttattgcttattaagcatgtactgttc-tgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
















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|151395057|gb|EV264928.1|EV264928
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|57575446|gb|CX548421.1|CX548421
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|31458202|gb|CD400230.1|CD400230
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|192333033|gb|FK024682.1|FK024682
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|11411884|gb|BF423895.1|BF423895
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|151406922|gb|EV276737.1|EV276737
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|9900944|gb|BE609912.1|BE609912
EST:     AAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: AAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|6725962|gb|AW310361.1|AW310361
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTT
EST: gi|192300730|gb|FG991112.1|FG991112
EST:     TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGAT                         GACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTTGT
genomic: TCATTCGCAAAGCTGTTCTGCGTATGCTGCCTAGAAACAAACTACGTGATgtaagtacta ... atggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTT-GT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaataactgatactaagttgcatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTTGATCGCCCACTTGAACCGTATGTGATGCCTCCTAGAAGCGTACGGGAAA
                                   attattgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatttggttagagctttttctgatatttttttgttccttataatattgaataactgatactaagttgcatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTTGATCGCCCACTTGAACCGTATGTGATGCCTCCTAGAAGCGTACGGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - gttcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agttgca