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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaagaagccaaaaaaagggaaatttatttctgttcattttattttaatttattttcattgttctgatacccgtgatactggtgttgtctttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG

Basic information

species Glycine max
transcript GLYMA16G29790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G29790.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 5
-------------------tagaagaagccaaaaaaagggaaatttatttctgttcattttattttaatttattttcattgtt--ctgatacccgtgatactggtgttgt----ctttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG
                    | | ||  |   |          | | || || ||| |||| || |  ||| |||| ||| |   ||||  ||   |   ||| | || |    | |  | |||||| ||||| || || ||||||||||| || |||||||||||||| ||||| || |||
gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactgaatccaacggc-ctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG
















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|192320556|gb|FK011966.1|FK011966
EST:     GCCCCATTGCAAACGTGCCCTATTTCAGAAGGGTGGCCTCTGCTCACCAA                         CTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGG
genomic: GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAAgtaattttca ... tttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
EST: gi|41146249|gb|CK606460.1|CK606460
EST:     GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAA                         CTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
genomic: GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAAgtaattttca ... tttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
EST: gi|58024886|gb|CX711627.1|CX711627
EST:     GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTGTGCTCACCAA                         CTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
genomic: GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAAgtaattttca ... tttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
EST: gi|10256359|gb|BE824125.1|BE824125
EST:     GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAA                         CTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
genomic: GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAAgtaattttca ... tttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
EST: gi|31471135|gb|CD413163.1|CD413163
EST:     GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAA                         CTTCACCATTCGGCCAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
genomic: GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAAgtaattttca ... tttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
EST: gi|9899031|gb|BE607999.1|BE607999
EST:     GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAA                         CTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA
genomic: GCCCCATTGCAAACGTGCCCTATCTCAGAAGGGTGGCCTCTGCTCACCAAgtaattttca ... tttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttattttcattgttctgatacccgtgatactggtgttgtctttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG
                 ttctgat  putative branch site (score: 3)
                                        ttgtcttt  putative PPT
     ttattttcattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaagaagccaaaaaaagggaaatttatttctgttcattttattttaatttattttcattgttctgatacccgtgatactggtgttgtctttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - -aaaaaaa
- - - - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg