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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaacctatatctctgcgttgcttttggtctaaatatcaatttagagatttagcattcatgcttacatgatcagaatgtccttgtccgaattgtcccaatatagctcttatgatatgcatgctaactttgcacctgataccattggtattttgtatctattataacctccttttttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTC

Basic information

species Glycine max
transcript GLYMA02G04120.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 11
gtaattaacctatatctctgcgttgcttttggtctaaatatcaatttagagatttagcattcatgcttacatgatcagaatgtccttgtccgaattgtcccaatatagctcttatgatatgcatgctaactttgcacctgataccattggtattttgtatctatta-taacctccttttttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTC
                                                                                        | | ||   |     | ||     ||   |   ||| |  |         || |    ||  | |  |  | || | | |||   | |   || | | ||||||||||||||||||||||||||||  |||||||||||||| || |||||||| ||||| |||||||||||||||||||| || |||| ||| |||||||
---------------------------------------------------------------------------------------tttcaaaacattatggttta--ctgtaaagtgctcattcacaaaccaattttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC
















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|18735196|gb|BM528624.1|BM528624
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTACGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGACCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|14206380|gb|BG840058.1|BG840058
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCNTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|57575455|gb|CX548430.1|CX548430
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|23734638|gb|BU765558.1|BU765558
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|9564586|gb|BE474095.1|BE474095
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|192305538|gb|FG994304.1|FG994304
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|4397575|gb|AI496572.1|AI496572
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|6725270|gb|AW309669.1|AW309669
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|58016426|gb|CX703168.1|CX703168
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|10253979|gb|BE821689.1|BE821689
EST:     GTGCACCCAAAGAAGAGGAGNNCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|209701248|gb|BW652226.1|BW652226
EST:     CAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: CAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|19453151|gb|BM954561.1|BM954561
EST:     GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
genomic: GTGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATTGATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGA
EST: gi|6134504|gb|AW132897.1|AW132897
EST:     TGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAAAGTTGTAATTTGAT                         TGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGG
genomic: TGCACCCAAAGAAGAGGAGGTCTTGCAGTATGCCAGAGTTGTAATT-GATgtaattaacc ... ttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacctgataccattggtattttgtatctattataacctccttttttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTC
                              ttataac  putative branch site (score: 2)
                          tctattataacctcct  CT-rich tract
                 tattttgtatctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaacctatatctctgcgttgcttttggtctaaatatcaatttagagatttagcattcatgcttacatgatcagaatgtccttgtccgaattgtcccaatatagctcttatgatatgcatgctaactttgcacctgataccattggtattttgtatctattataacctccttttttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC