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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaatcaaatgcttgtgaaatataagttttatccatcttccattccacctactccaccattcaattttttttttaactttttaatgtttccttatgtatggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAAATTATATCCTGGGCATCGCCGAGAAGAAATACAACATTGTATCGATAAA

Basic information

species Glycine max
transcript GLYMA01G00430.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 14
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagcaatcaaatgcttgtgaaatataagttttatccatcttccattccacctactccaccattcaattttttttttaactttttaatgtttccttatgtatggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAAATTATATCCTGGGCATCGCCGAGAAGAAATACAACATTGTATCGATAAA
                  || |   |  ||  |  |||||         || ||  |  | | |    | | ||||  || ||| |  || |     |     | | | |||||| ||||||||||||||||| || || |||||||||  ||||||| | ||  | |||||||| |||||     | ||| || |  | || || || || 
------------------gtaaggcactagcatattccattgattgaatcatctggttaatcttattttatgttttgcaaatttctcttgatgtgcaagaatggttctgtagTTACGTGGAATGTACATCAGCTGCTATCCAAGCTTTGATATCATTTCGAAAGCTGTATCCTGGTCATCGAAAGAAGGAAGTAGATGAGTGCATTGAGAAG

upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 14
gtaagcaatcaaatgcttgtgaaatataagttttatccatcttccattccacctactccaccattcaattttttttttaactttttaatgtttccttat---gtatgg-tgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAAATTATATCCTGGGCATCGCCGAGAAGAAATACAACATTGTATCGATAAA
                          |||| | |   ||  ||   |    |    | ||  ||||  || ||| |  |||||| || | | ||  ||     ||||  | | |||||| ||||||||||||||||| ||  ||||||||||| |||||||||  ||||| ||||| ||||||||  ||||||||||| ||||||||||  | |||
-------------------------gtaagatattggcactttgattaatgctatttgcaatattcttttgtttatgcaactttatagtttatctctaactaatatgactatgtagTTACGTGGAATGTACATCAGCTGCACTTCAAGCTTTGACATCATTTAATAAATTTTATCCGGGGCATCGGAGAGAAGAAATAGAACATTGTATTAAAAAA
















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|18733901|gb|BM527876.1|BM527876
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGAT
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGAT
EST: gi|22524821|gb|BU083632.1|BU083632
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|42723073|gb|CK768972.1|CK768972
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|18732433|gb|BM527041.1|BM527041
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|51344264|gb|CO984997.1|CO984997
EST:     ACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|19269470|gb|BM885726.1|BM885726
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|13789963|gb|BG652554.1|BG652554
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|10253317|gb|BE821083.1|BE821083
EST:     AGATAATCAATCNTGCTGAAACTTTTGNNGACATCGTTATTGANTATNC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTNNNGCATCATTTAGGAA
genomic: AGATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
EST: gi|24136389|gb|BU926899.1|BU926899
EST:     ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCC                         TTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA
genomic: ATAATCAATCCTGCTGAAACTTTTGGTGACATCGTTATTGATTATCCgtaagcaatc ... tggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaccattcaattttttttttaactttttaatgtttccttatgtatggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAAATTATATCCTGGGCATCGCCGAGAAGAAATACAACATTGTATCGATAAA
     attcaatttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaatcaaatgcttgtgaaatataagttttatccatcttccattccacctactccaccattcaattttttttttaactttttaatgtttccttatgtatggtgtatagTTATGTGGAATGTACATCAGCAGCGATTCAAGCTTTGGCATCATTTAGGAAATTATATCCTGGGCATCGCCGAGAAGAAATACAACATTGTATCGATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA