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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaatgtttggtctgagacctgattttaaagttttattgttgttttattactttctttatacgttattttatctttttcttttctggttaactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCTGCTCGCAGGTCCAGGTTGCGCAAGCAG

Basic information

species Glycine max
transcript GLYMA09G34170.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34170.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G32150.1 (Arabidopsis thaliana), 3'ss of exon 10
ttttaatgtttggtctgagacctgattttaaagttttattgttgttttattactttctttatacgttattttatctttttcttttctggttaactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCTGCTCGCAGGTCCAGGTTGCGCAAGCAG
                  |     || |   | | ||| |  |  ||||    | ||     |   | ||| ||  ||||        || || |  |||||||| |||||| ||||  | || || |||||||| || || |||||||||||||| || ||||||||||| || |||
------------------gtaagtatctcctaatcttacttctcctttacgtttatccaagcagcgtgtttgattgtttt--------gtgaaat--cagGATGAGAGAGAGATTAAGCGACAGAGACGGAAGCAATCCAATAGGGAATCTGCTCGTAGATCCAGGTTGCGTAAACAG

upper sequence: GLYMA09G34170.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv02s0012g02250.t01 (Vitis vinifera), 3'ss of exon 10
ttttaatgtttggtctgagacctgattttaaagttttattgttgttttattactttctttatacgttattttatctttttctttt--ctggttaactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCTGCTCGCAGGTCCAGGTTGCGCAAGCAG
|   |   |  || ||      |  |||||| |||  ||  || ||   ||| | |  || |  | |||||||| |    ||||   ||   |    ||||||||||||||||||||||||| || ||  | |||||||| ||| |||| ||||||||| | ||||||||||| ||||||
tgacaccttcgggcctttttttttcttttaatgttc-atgcttattcccttattattattgt-tgctattttatttgacactttgaacttactttgattcagGATGAAAGAGAGCTTAAAAGACAGAGAAGAAAGCAGTCGAACCGGGAGTCTGCTCGCCGATCCAGGTTGCGTAAGCAG
















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|31473646|gb|CD415674.1|CD415674
EST:     TGGTTACTGTTGGATCACGGGATAGTGCTCAGTCACAACTCTGGCTACAG                         GATGAAAGAGAGCTTAAAAGGCCAAGGCGGAAACAGTCTAACAGGGAATCT
genomic: TGGTTACTGTTGGATCACGGGATAGTGCTCAGTCACAACTCTGGCTACAGgttatttttt ... taactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCT
EST: gi|20498852|gb|BQ273782.1|BQ273782
EST:     TGGTTACTGTTGGATCACGGGATAGTGCTCAGTCACAACTCTGGCTACAG                         GATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCT
genomic: TGGTTACTGTTGGATCACGGGATAGTGCTCAGTCACAACTCTGGCTACAGgttatttttt ... taactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCT
EST: gi|254313915|gb|GR831544.1|GR831544
EST:     TGGTTACTGTTGGATCACGGGATAGTGCTCAGTCACAACTCTGGCTACAG                         GATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCT
genomic: TGGTTACTGTTGGATCACGGGATAGTGCTCAGTCACAACTCTGGCTACAGgttatttttt ... taactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattactttctttatacgttattttatctttttcttttctggttaactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCTGCTCGCAGGTCCAGGTTGCGCAAGCAG
                                          ggttaac  putative branch site (score: 3)
                       ttttatctttttcttt  CT-rich tract
            tttatacgttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaatgtttggtctgagacctgattttaaagttttattgttgttttattactttctttatacgttattttatctttttcttttctggttaactttcagGATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCTGCTCGCAGGTCCAGGTTGCGCAAGCAG

- - -atgtttg
- - - - - - - - - - cctgatt
- - - - - - - - - - - - - - - - - - - -tgttgtt