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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tactgtatatagtttaactacaaaatttacatccatgctcaattcattctaattgtttcttggtgagttcctcaggtttaatttttaacatattttcatcgcatttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACGTGGTGGTCGTTGAGTTGCACCTTTCTTCATTTTTGTGGCATGTGGTTAT

Basic information

species Glycine max
transcript GLYMA18G52210.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 3
tactgtatatagtttaactacaaaatttacatccatgctcaattcattctaattgtttcttggtgagttcctcaggtttaatttttaacatattttcatcgcatttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACGTGGTGGTC-GTTGAGTTGCACCTTTCTTCATTTTTGTGGCATGTGGTTAT
                | | || | ||  | |      |  || | || | || | ||  |       |  | |   ||  |||||||    | |       |  ||||||    ||| |||| ||||| || ||  | || ||||| ||||| ||||| || ||  |   |||   ||| |   |||    || ||||  | | |||||||
--------------gtattgcatatttcccttttgacttatataccttgtgatagattaata-----ctttttaaaatttttttttaatgcctct-----ataaatccagGACGGCCTATGGGGCGTGGTCGGGGCCGTGGGCGTGGACGTGGACGTGGTCGAGGCCGCTAGTTACCTTGTAG--TTCAAATTTCTTGTCACTTCTGGTTAT
















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|17519318|gb|BM188360.1|BM188360
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
EST: gi|192328861|gb|FK023263.1|FK023263
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
EST: gi|31473009|gb|CD415037.1|CD415037
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGTCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
EST: gi|298192082|gb|HO036164.1|HO036164
EST:     CTGCTTGTGGAAGAGACACCTAAGATCATACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACG
EST: gi|23728045|gb|BU762064.1|BU762064
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
EST: gi|33388742|gb|CA851949.1|CA851949
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGTCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
EST: gi|298175521|gb|HO018232.1|HO018232
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGTCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG
EST: gi|298174943|gb|HO014860.1|HO014860
EST:     CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGG                         GAAACCTTTGGGACGTGGACGAGGAAGGGGTCGTGGGCGTGGGCGTGGACG
genomic: CTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatat ... catttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttggtgagttcctcaggtttaatttttaacatattttcatcgcatttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACGTGGTGGTCGTTGAGTTGCACCTTTCTTCATTTTTGTGGCATGTGGTTAT
                          ttttaac  putative branch site (score: 2)
                                             catttcc  putative PPT
                    tttaatttttaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtatatagtttaactacaaaatttacatccatgctcaattcattctaattgtttcttggtgagttcctcaggtttaatttttaacatattttcatcgcatttccaggGAAACCTTTGGGACGTGGACGAGGAAGGGGCCGTGGGCGTGGGCGTGGACGTGGTGGTCGTTGAGTTGCACCTTTCTTCATTTTTGTGGCATGTGGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG