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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaacgtgtcaggttagcgtaatgtaggattgaaacggcacttttttttgcagtgtttgtgagataatttatgcaaaaattgcgtgtttgttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATTGTCACGCCACGATCTACGTGTGATGTTATCG

Basic information

species Glycine max
transcript GLYMA05G04580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G04580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0154g00500.t01 (Vitis vinifera), 3'ss of exon 2
tcaaacgtgtcaggttagcgtaatgtaggattgaaacggcacttttttttgcagtgtttgtgagataattt--atgcaaaaattgcgtgtttgtt--ttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATTGTCACGCCACGATCTACGTGTGATGTTATCG
  |||  | ||      ||  ||   ||| |  ||| |  | | |   ||    | ||| ||  || ||    ||    ||||| ||   |||||  | || ||||||||||||| ||||||||||||||||||||||||||||| || || ||||||  ||| || || || |||||  |  | |
--aaaattttcttagcggccaaacagagggt-aaaatgcaaatgtagattttgat-tttctgccatgatcgggatatttaaatttcgaaattgttcgtgttcagGTGAAAACAACGAATCCGAAGAAGTATTGTGTTCGTCCGAATACCGGAATTGTCTTGCCTCGGTCGACATGTGACATCTTAG
















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|298197354|gb|HO044833.1|HO044833
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|298187165|gb|HO034314.1|HO034314
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|7925879|gb|AW831905.1|AW831905
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTAGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGGGTT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|192326599|gb|FK018846.1|FK018846
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|8283114|gb|BE020675.1|BE020675
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|193469921|gb|FK437262.1|FK437262
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|298194582|gb|HO043054.1|HO043054
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|7588116|gb|AW703919.1|AW703919
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|192320302|gb|FK013392.1|FK013392
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTAGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGGGTT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|33390081|gb|CA853288.1|CA853288
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|209700050|gb|BW656218.1|BW656218
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|298185938|gb|HO031099.1|HO031099
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|192324904|gb|FK015385.1|FK015385
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|18041004|gb|BM309298.1|BM309298
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|10848335|gb|BF070847.1|BF070847
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|298189123|gb|HO037526.1|HO037526
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTAGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGGGTT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|10843377|gb|BF067174.1|BF067174
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT
EST: gi|298169114|gb|HO020474.1|HO020474
EST:     CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTAGCCTTCAAG                         GTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGGGTT
genomic: CATGTTCTCTTCAATTGTCCAATAAGACCGATAGCTATGTGGCCTTCAAGgtaattttaa ... gttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcagtgtttgtgagataatttatgcaaaaattgcgtgtttgttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATTGTCACGCCACGATCTACGTGTGATGTTATCG
                                          tttgtttttt  CT-rich tract
                   ataatttatgcaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaacgtgtcaggttagcgtaatgtaggattgaaacggcacttttttttgcagtgtttgtgagataatttatgcaaaaattgcgtgtttgttttttaagGTGAAAACAACCAATCCGAAGAAGTATTGTGTTCGTCCGAACACTGGTATTGTCACGCCACGATCTACGTGTGATGTTATCG

- - - - - - - - - - -aatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgtgt