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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacatcacttcattttattaaaatacttagttatgaccattgtagttagcaaacagtttccgtgacaggcaatttcttaattggtgtcatgattcacgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT

Basic information

species Glycine max
transcript GLYMA02G01930.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 12
gtagacatcacttcattttattaaaatacttagtt-atgaccattgtagttagcaaacagtttccgt---gacaggcaatttcttaattg-gtgtcatgattcacgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT
            || |||  || |||||   | || |   ||| || | || |  |     ||  ||   ||  || |  ||   ||||     | ||| ||      || ||||| ||||| || |||||||   ||||||| ||||| || ||||| ||||||||| | ||||| || ||||||||||||||   | |  | ||    
------------tcctttcgttgaaatatgcaatttacttccactgaaatttgtgatttacttttgtgctgattggaagattggaaattccaaataatggttgttt--ttgcagGTTATGGGTAATCATGTTGGTGTCACAGTAGGTGGTTCGAATGGACATTTTGAGTTGAATGTCTTTAAGCCAATGATTGCAGCTGGATTACTTAGA

upper sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 13
gtagacatcacttcattttattaaaata--cttagttatgaccattgtagttagcaaaca-gtttccgtgacaggcaatttcttaattggtgtcatgattcacga-atttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT
       | | | |  | ||| || | |  ||||||   ||||| || |  |||     | | ||   | |  |    ||   |  |||| ||    |   |  | ||| ||||| |||||||||||||| ||  | ||||| ||||| |||||||||||||| ||  | ||||| ||||||||  |||| || | |  |||  | |||
------gtaagtcccatctatcaatacattcttagtacagaccaatgaatctagatgctaaggttgtattattgttccttgactgtttgg-gttgcaaccaataacattgcagGTTATGGGAAACCATGTAGCTGTGACAGTTGGTGGGTCAAATGGTCATTTCGAATTGAATGTATTCAAGCCGGTGATCGCGAGTGCTCTTTTACAT

upper sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 13
gtagacatcacttcattttattaaaatacttagttatgaccattgtagttagcaaacagtttccgtgacaggcaatttcttaattggtgtcatgattcacgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT
      || |   | |||| ||    |      ||||    ||| |  | |  |||     | |    | ||   |     |||     |  |  |  |    || ||||| |||||||| || || || || || || ||||||||||| |||||||||||||| ||||| ||||||||  ||||||| | | ||||||| | |
----ttattagaacctttttttgtggttgact-ttatatttatt-tgttcaaaaaattagcttctaatctggt--tcgaccaatcaaaatttttgtata-atcttgcagGTTATGGGAAATCACGTGGCCATTACTGTAGGTGGATCAAACGGTCATTTTGAGCTGAATGTATTCAAGCCTCTGATTGCTAGTGGTCTCCTACGT

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|51344356|gb|CO985089.1|CO985089
EST:     GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG                         GTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
genomic: GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatca ... cgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
EST: gi|26047345|gb|CA784166.1|CA784166
EST:     GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG                         GTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
genomic: GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatca ... cgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
EST: gi|192307576|gb|FG999615.1|FG999615
EST:     GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG                         GTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
genomic: GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatca ... cgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
EST: gi|51336381|gb|CO980247.1|CO980247
EST:     GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG                         GTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
genomic: GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatca ... cgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
EST: gi|151394627|gb|EV264498.1|EV264498
EST:     GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG                         GTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
genomic: GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatca ... cgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
EST: gi|51343889|gb|CO984622.1|CO984622
EST:     GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG                         GTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT
genomic: GGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatca ... cgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtttccgtgacaggcaatttcttaattggtgtcatgattcacgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT
                       tcttaat  putative branch site (score: 3)
                   aatttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacatcacttcattttattaaaatacttagttatgaccattgtagttagcaaacagtttccgtgacaggcaatttcttaattggtgtcatgattcacgaatttcagGTCATGGGAAACCATGTTGCAATCACAGTGGGTGGATCAAATGGTCATTTTGAGCTCAATGTGTTCAAGCCAATGATTGCCAATTGTCTCCTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA