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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaatttgaacatttgaatggcgttaatgtgtag

Basic information

species Glycine max
transcript GLYMA16G33240.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 5'ss of exon 1
TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaatttgaacatttgaatggcgttaatgtgtag
       | | ||    |    |||  |   | ||| |  |  |  |    |||  |  || |  |||||||| || ||||||| ||||||||||||||||| | |    | | || ||             || | |   ||  |||||  | |    | | || | ||   ||||   ||||  ||||  ||   ||          
-------GAGATTACGCCGC--TCATTTTTAGGGTTTCAGATATAGGCAGATTC--TCACATTTGCAAACATGACGACTCAGATCAGCAAGAAGAGAAAGgtgaatt---gtgtgattctg--ttcattttgttctttcaatggatttatcgtattggaactgttttggtaactgtg---ttgag-attttgattttgtag--------

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 1
TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGT-CAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaa---tttgaacatttgaatggcgttaatgtgtag
               |  ||  |  |     |  |   | |    ||  |    || || |   | ||||||||||| |||| ||||||||||||||||||||  |           |||  |         ||||||  ||  | | |    |  |         ||| ||| ||| ||   || |   | ||   | |  ||    |  ||
---------------ATTAGGGTTTGCAAAAGCATAGAG-AAACCCGAGCTCAGATCTCAAACCTGCAAACATGGCGACTCAAATGAGCAAGAAGAGAAAGgtctg-----------atcatatgttcttttattttcctttgttttctgagctaccaatcggaaagttatgtttgttaaagtttcggtaacttattttgttttctcttacag

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 1
TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaatttgaacatttgaatggcgttaatgtgtag
                                              | | |  | ||  | |       ||||||| ||||||| |||||||||||||||||  ||               || ||    |  |  ||   | || || | | |||                                                     
----------------------------------------------GCTAGGGCTTTGGCGG-------CATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgtc--------------aagcaatgccgctccct-cctctgattctctcttccag--------------------------------------------------

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 1
-TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGTCAA--ACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaatttgaacatttgaatggcgttaatgtgtag
  || ||||  |    |   |    |   | |       |  |  |  || |  |   |   |  |      ||||||| ||||||| |||||||||||||||||  || |        | | |   |     |   ||||  |    |||  || |||                                                     
GGCATACTGCATAATAATTTGTCAAAAGCCCTAGAA---GAGCCCTAATTAGGACGGCTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttc--------agcaatgccgctctccccttctgctctgatttgattcttccag--------------------------------------------------

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|151410450|gb|EV280265.1|EV280265
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|298190501|gb|HO032622.1|HO032622
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACAAGGTTCTGACTCGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|20812287|gb|BQ296765.1|BQ296765
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACTCGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|24135528|gb|BU926038.1|BU926038
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACTCGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|4313574|gb|AI460693.1|AI460693
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|6566862|gb|AW234494.1|AW234494
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACTCGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|193341426|gb|FK308388.1|FK308388
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|208306439|gb|GE104448.1|GE104448
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT
EST: gi|209709418|gb|BW668360.1|BW668360
EST:     GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAG                         TTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACTCGT
genomic: GTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgcta ... taatgtgtagTTTGTTGCGGACGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACACTGTGTTTGGAGCAGAATCAGATCGTGTGTTCCGTACGTTCGTTCGTTCATTTCCAGTGTCAAACATGGCGTCTCAGATGAGCAAGAAGAGAAAGgtaagtgctagagagaatcgaaaacagcagcattttctatttgtgtttattttttcttcattcttgttgtgtatgtgaatttgaacatttgaatggcgttaatgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA