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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttaacactaggctcataggaacagcatgagcagtttgtttgtcattaggatgttactatgtgtttatagaagcttttattaatgcaattatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGTGCCCGCAAGCCTAGTCTGTTGCTCTCAACCATGAGGGCTTTGGATAACC

Basic information

species Glycine max
transcript GLYMA06G17330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g00330.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------gttttaacactaggctcataggaacagcatg----agcagtttgtttgtcattaggatgttactatgtgtttatagaagcttttattaatgcaattatac-atagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGTGCCCGCAAGCCTAGTCTGTTGCTCTCAACCATGAGGGCTTTGGATAACC
                                                                             || || |   |    |  || | ||   ||      || || ||| | |   | |  || || ||| ||| |   |  || | |    || |  || | |  |||||||| ||| ||    | || ||||| ||||| |||||||||||||| |||| |||||  ||  |||| |||||||| |||||||||||| |||| | ||
gtaagactcgctttcttgttcctcattctgtttctaccgctgaaaactttaggtgcagttttgttcatgacctcattgtattcatcgttcatttgtatgcactttatctattggcggtatgtctatgcattgagtgata-tatctgtctgaggtggcatctt---atacggttgtgctgtagGTTGAAGTTAGGGCAAGAGAGGGAAGAGCTGTAAACATCCACATGTTCTGTGGCCGCAGACCAGGTCTATTGCTCTCCACCATGAGGGCTCTGGACAGCC
















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|208323336|gb|GE118323.1|GE118323
EST:     TGGCCAACCTGCTAGG                         GTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
genomic: TGGCCAACCTGCTAGGgtaatgttct ... ttatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
EST: gi|7925024|gb|AW831050.1|AW831050
EST:     AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTANG                         GTTGAGGTTCGGCTGCGCGAAGGAAGG
genomic: AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGGgtaatgttct ... ttatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGG
EST: gi|19346482|gb|BM891362.1|BM891362
EST:     AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGG                         GTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
genomic: AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGGgtaatgttct ... ttatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
EST: gi|208026815|gb|GD823995.1|GD823995
EST:     AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGG                         GTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
genomic: AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGGgtaatgttct ... ttatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
EST: gi|208194412|gb|GD992511.1|GD992511
EST:     TGGCCAACCTGCTAGG                         GTTTGAGGTTCGGCTGTCGCGAAGGAAGGGCTGTTAACATCCACATGTTTT
genomic: TGGCCAACCTGCTAGGgtaatgttct ... ttatacatagG-TTGAGGTTCGGCTG-CGCGAAGGAAGGGCTGTTAACATCCACATGTTTT
EST: gi|192331995|gb|FK024525.1|FK024525
EST:     AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGG                         GTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
genomic: AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGGgtaatgttct ... ttatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
EST: gi|51341831|gb|CO983148.1|CO983148
EST:     AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGG                         GTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT
genomic: AAGAACTGTGCCCCAGCTCATTGCCCAGCCCCAATGGCCAACCTGCTAGGgtaatgttct ... ttatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaggatgttactatgtgtttatagaagcttttattaatgcaattatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGTGCCCGCAAGCCTAGTCTGTTGCTCTCAACCATGAGGGCTTTGGATAACC
                                  tattaat  putative branch site (score: 2)
                               ttttattaatgcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttaacactaggctcataggaacagcatgagcagtttgtttgtcattaggatgttactatgtgtttatagaagcttttattaatgcaattatacatagGTTGAGGTTCGGCTGCGCGAAGGAAGGGCTGTTAACATCCACATGTTTTGTGCCCGCAAGCCTAGTCTGTTGCTCTCAACCATGAGGGCTTTGGATAACC

- - - - - - - - - - - - - gcatgag
- - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - ggatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa