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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagtcacgaatatttctttctatcatgattattgtattttctgttaagagtttatgactggatggagttaagcaattaatgcaaggtgcttttttgcagGCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG

Basic information

species Glycine max
transcript GLYMA09G29070.1
intron # 2
splice site 3'
intron type U2

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|151400617|gb|EV270431.1|EV270431
EST:     TCCGCTTGGGAATCTCAT                         GCCATATTTCCTCGCATATTTGGCCACGAAGCATCATG
genomic: TCCGCTTGGGAATCTCATgtaagtcttg ... ttttttgcagGCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG
EST: gi|298197385|gb|HO044864.1|HO044864
EST:     TTGTCTCCACCTCTCTCTGTCGCAGTGGTCTCTCCGCTTGGGAATCTCAT                         GCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG
genomic: TTGTCTCCACCTCTCTCTGTCGCAGTGATCTCTCCGCTTGGGAATCTCATgtaagtcttg ... ttttttgcagGCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG
EST: gi|209727032|gb|BW680326.1|BW680326
EST:     TTGTCTCCACCTCTCTCTGTCGCAGTGATCTCTCCGCTTGGGAATCTCAT                         GCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG
genomic: TTGTCTCCACCTCTCTCTGTCGCAGTGATCTCTCCGCTTGGGAATCTCATgtaagtcttg ... ttttttgcagGCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagagtttatgactggatggagttaagcaattaatgcaaggtgcttttttgcagGCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG
                             aattaat  putative branch site (score: 3)
                                          tgctttttt  putative PPT
                             aattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagtcacgaatatttctttctatcatgattattgtattttctgttaagagtttatgactggatggagttaagcaattaatgcaaggtgcttttttgcagGCCATATTTCCTCGCATATTTGGCCACGAAGCATCAGG

- - - - - - - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaagg