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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcaatgcttattattattatcttaacaaacgtagaaccttctcttgctttctcaattgagatgcatcatatattttaaaatctgtttttctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGAGAACCACTATATGCTAAGTTTCGACTTCGTGAACCATACAAGATGCCAA

Basic information

species Glycine max
transcript GLYMA20G24100.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 3
----attcaatgcttattat-tattatcttaacaaacgtagaaccttctcttgctttctcaattgagatgcatcatatatt-ttaaaatctgtttttctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGAGAACCACTATATGCTAAGTTTCGACTTCGTGAACCATACAAGATGCCAA
     || ||    | || | | |||||| |    || |   |  || |    |||  || ||    |||   |    ||  | | ||||   |||||| || ||| || |||| |||||||||||||||||||| |||||||| ||||||||  | || ||  ||  ||| |||||||| ||||||||||||| ||  |||||||
attttttgaaattgtgttttgtgttatct-agttgacttg--atgttgtgcatcttaatctatgagtatgttcctctaatggtcagaatc---ttttcttttacagATTACTAGGTCTATTGGTGATGTATATTTAAAAAAGGCTGAGTTCAACAGGGAGCCTTTAATTGCCAAGTTTCGCCTTCGTGAACCATTCAGAATGCCAA
















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|208064027|gb|GD862013.1|GD862013
EST:     TGAAGGGTCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATAGA
genomic: TGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|10238100|gb|BE806988.1|BE806988
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGTCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAA
EST: gi|17519473|gb|BM188515.1|BM188515
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|18725738|gb|BM523643.1|BM523643
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGTCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATAGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|6341594|gb|AW164418.1|AW164418
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATNTGAAAAAGGCCGAGTTCAATCGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|308098935|gb|HO760776.1|HO760776
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|308098964|gb|HO760805.1|HO760805
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGTCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATAGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|208175401|gb|GD976796.1|GD976796
EST:     TATTGTGGTTTTTAAAGCATAATGTATGGCGTGTGAAGGGTCTTATTCAA                         GCTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATAGA
genomic: TATTGTGG-TTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|192294523|gb|FG987452.1|FG987452
EST:     GGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
genomic: GGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|193308667|gb|FK275362.1|FK275362
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGA
EST: gi|254340610|gb|GR854338.1|GR854338
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGTCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATAGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|18038853|gb|BM307147.1|BM307147
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
EST: gi|298165586|gb|HO011635.1|HO011635
EST:     ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAA                         GTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA
genomic: ATATTGTGGTTTTAAAGCATAATGTATGGCGTGTGAAGGGCCTTATTCAAgtaagtcact ... tctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctttctcaattgagatgcatcatatattttaaaatctgtttttctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGAGAACCACTATATGCTAAGTTTCGACTTCGTGAACCATACAAGATGCCAA
                                     tctgtttttctgtt  CT-rich tract
                     atcatatattttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcaatgcttattattattatcttaacaaacgtagaaccttctcttgctttctcaattgagatgcatcatatattttaaaatctgtttttctgttgcagGTTTCTAGATCTATTGGTGATGTATATTTGAAAAAGGCCGAGTTCAATCGAGAACCACTATATGCTAAGTTTCGACTTCGTGAACCATACAAGATGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcat