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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaccttcagtattctttaaaacttctctgtttttttttttgaaagaaattcatttaacctgcaccttattttgctttgctatgtatccataagattcagGAAACTGATGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCCCAATATTTTGGAGATCAGAACAAGGCTGCAGATGTGGATTCTCAAG

Basic information

species Glycine max
transcript GLYMA08G36700.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G46750.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgaccttcagtattctttaaaacttctctgtttttttttttgaaagaaattcatttaacctgcaccttattttgctttgctatgtatccataagattcagGAAACTGATGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCCCAATATTTTGGAGATCAGAACAAGGCTGCAGATGTGGATTCTCAAG
 | |     ||| |  |||  |||    |||           || ||||||  |||     | |  |||  ||| | |   |   | |   | || || | ||||| ||||||||||||| |||||| ||||| || ||||| ||||| ||  |||||| ||| ||| |||||||||  | ||| ||| | || |      
gtaaagaaaagtttcatttttaacagaactgaagaaag---agatagaaatcaattctcgattcctctttgtttacctgttttctttttacttagGTTGAAGAAACAGATGAAGCAAGAAAGAAGTTTTCAAACGCCAAATCGATTTCCTCTGCCCAATTTTTCGGAAATCAGAACAGAGATGCCGATCTTGACT------

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 4
tgaccttcagtattctttaaaacttctctgtttttt-----tttttgaaagaaattcatttaacctgcacctta-ttttgctttgctatgtatc---cataagattcagGAAACTGATGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCCCAATATTTTGGAGATCAGAACAAGGCTGCAGATGTGGATTCTCAAG
    | ||| || | ||| |   |  | ||||   |     |||      |||     ||   ||| ||    | |||   | |   || || |    || ||||| |||||| ||||||||| || ||||||||||||||||| |||||||| || ||| |||||||||| || |||| ||  || ||    ||  |||| |      
---acatcattactatttcagtttattgtgttagctgtaaatttgcatgtgaagcatgttcttcctccagtacaatttcattcttacatctaacaattatcagATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACT------
















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|13789933|gb|BG652524.1|BG652524
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|13789933|gb|BG652524.1|BG652524
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|13789933|gb|BG652524.1|BG652524
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|13789933|gb|BG652524.1|BG652524
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|13789933|gb|BG652524.1|BG652524
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|13789933|gb|BG652524.1|BG652524
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|58017014|gb|CX703756.1|CX703756
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|58017014|gb|CX703756.1|CX703756
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|298194738|gb|HO043210.1|HO043210
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|298194738|gb|HO043210.1|HO043210
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|57575109|gb|CX548084.1|CX548084
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|57575109|gb|CX548084.1|CX548084
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|58015077|gb|CX701819.1|CX701819
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|58015077|gb|CX701819.1|CX701819
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAATTCA                     
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGC--A---Agtaagccata ... taagat
EST: gi|15813255|gb|BI785530.1|BI785530
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|15813255|gb|BI785530.1|BI785530
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|15813255|gb|BI785530.1|BI785530
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|15813255|gb|BI785530.1|BI785530
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|15813255|gb|BI785530.1|BI785530
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-
EST: gi|15813255|gb|BI785530.1|BI785530
EST:     TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAA                         A
genomic: TGGATAGTGGCTTTCCAAAGAAATCTGGGCCAAGCTCCTCCAAAGTGCAAgtaagccata ... taagattcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattcatttaacctgcaccttattttgctttgctatgtatccataagattcagGAAACTGATGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCCCAATATTTTGGAGATCAGAACAAGGCTGCAGATGTGGATTCTCAAG
       atttaac  putative branch site (score: 3)
                     ttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaccttcagtattctttaaaacttctctgtttttttttttgaaagaaattcatttaacctgcaccttattttgctttgctatgtatccataagattcagGAAACTGATGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCCCAATATTTTGGAGATCAGAACAAGGCTGCAGATGTGGATTCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- accttca
- - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgta