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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgtgtaatagagtcacttctactctataaatatctattctagttcaactactgagtagttaatgaaaatgcttttttctttttttttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG

Basic information

species Glycine max
transcript GLYMA16G27210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G24170.1 (Arabidopsis thaliana), 3'ss of exon 3
aattgtgtaatagagtcacttctactctataaatatctattctagttcaactactgagtagttaatgaaaatgcttttttctttttttttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG
          ||   ||  |  |  |  || |  |    ||  | |   ||     |  |  | ||     |  || ||||   ||||||    |   || |||||||| |||||||||||||| ||||||||| | |||||||||||  |||  || ||||| ||||||
---------gtaagttccttgttgatgcattatcaaacgttggaatcttac-----acgatcttatacctttatttgtttccactttttttggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTACTTACGGTGGTGAACTTGAG

upper sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 4
aattgtgtaatagagtcacttctactctataaatatctattctagttcaactactgag--tagttaatgaaaatgcttttttctttttt-tttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG
   ||| |  ||||     |       ||   ||   ||||  |  | || | ||||   ||     | | | ||   |    | |    | |   ||   ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||| |||||||  |||||
-tctgtttgttaga--tgttgaattagtaatgatggttattgcaaatgaaattctgaaactaaaatttcatattgtcatgacgtctcacatctgggtttgcagGTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTTTGGTGTATGGAGCATCTTTTAGAGGTGAAATTGAG
















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|207720502|gb|GD703141.1|GD703141
EST:     CTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAAC                         GTGTGTTATTCG
genomic: CTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAACgtaagttata ... aatttcaaagGTGTGTTATTCG
EST: gi|27424557|gb|CA936077.1|CA936077
EST:     AATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAAC                         GTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATC
genomic: AATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAACgtaagttata ... aatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATC
EST: gi|193346232|gb|FK309724.1|FK309724
EST:     CTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAAC                         GTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATC
genomic: CTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAACgtaagttata ... aatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATC
EST: gi|151394106|gb|EV263977.1|EV263977
EST:     CTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAAC                         GTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATC
genomic: CTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAACgtaagttata ... aatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaactactgagtagttaatgaaaatgcttttttctttttttttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG
                                         ttttaat  putative branch site (score: 3)
                          tgcttttttctttttt  CT-rich tract
                ttaatgaaaatgcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgtgtaatagagtcacttctactctataaatatctattctagttcaactactgagtagttaatgaaaatgcttttttctttttttttaatttcaaagGTGTGTTATTCGTGGTTGTGTTCCCAAAAAGATTTTGGTCTATGGAGCATCTTTTGGAGGTGATCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - cttctac
- - - - - - - - - - - - - - - - - - - - - - - - -actactg