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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTGCAATTCCCTACTCGTGATTCCTTTGACCATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgctctacatgtatatctgttgcaaaaaaactaagttttttatttattttgaattggctaatgtttgatattttgtttctttttattgatatcag

Basic information

species Glycine max
transcript GLYMA19G18340.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G18340.5 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0040g02910.t01 (Vitis vinifera), 5'ss of exon 3
GTTGTTGCAATTCCCTACTCGTGATTCCTTTGACCATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgctctacatgtatatctgttgcaaaaaaactaagttttttattt---attttgaattggctaatgtttgatattttgtttctttttattgatatcag
| || ||||||||||| ||||  || ||||||| |||||  | || ||||||   |||||||||||||||||||||||||||||||||   |  |   ||  | |  | ||     |    | | ||| | |  ||   |  || | |   ||  || |||    || |                    
GATGGTGCAATTCCCTTCTCGGTATGCCTTTGATCATGCAATTAAGGTGATTAATAAGAAGGGTCGCTTGTACAAATTGGACAGGgtaatgtcattagcacatttcacagtatttgattggccatgttatgtcctttagaagttaactatactgttgcttggatgttag--------------------
















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|298163981|gb|HO013626.1|HO013626
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAA
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAA
EST: gi|57575654|gb|CX548629.1|CX548629
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|21675161|gb|BQ627512.1|BQ627512
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|151396560|gb|EV266437.1|EV266437
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|254316869|gb|GR828406.1|GR828406
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|17518794|gb|BM187836.1|BM187836
EST:     GATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: GATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|9203906|gb|BE330130.1|BE330130
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACANG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|298166366|gb|HO008603.1|HO008603
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCA
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCA
EST: gi|24135884|gb|BU926394.1|BU926394
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCA
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCA
EST: gi|9564251|gb|BE473760.1|BE473760
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGAC
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGAC
EST: gi|298172811|gb|HO019795.1|HO019795
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|6567025|gb|AW234652.1|AW234652
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|58014794|gb|CX701536.1|CX701536
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|58024651|gb|CX711392.1|CX711392
EST:     GTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: GTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
EST: gi|9204922|gb|BE331146.1|BE331146
EST:     ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGG                         GTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT
genomic: ATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgct ... ttgatatcagGTTAATCTTCACCAATGGGACCAAGTAAAACCATATGACGGAAAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTGCAATTCCCTACTCGTGATTCCTTTGACCATGCTGTAAAAGTGATTTTAAAGAAGGGTCGCTTGTACAAATTGGACAGGgtatgctgctctacatgtatatctgttgcaaaaaaactaagttttttatttattttgaattggctaatgtttgatattttgtttctttttattgatatcag

- - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG