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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattatgctggatatgtttgtctccttaagctattgagtttagatttttagatctatctgaggctgagctaattttatacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTCTCATGGGCTCTATCTTTCAGTGCTTAAATCCTGCCTTAACTATTGCTGC

Basic information

species Glycine max
transcript GLYMA02G35240.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatattatgctggatatgtttgtctccttaagctattgagtttagatttt-tagatctatctgaggctgagctaattttatacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTCTCATGGGCTCTATCTTTCAGTGCTTAAATCCTGCCTTAACTATTGCTGC
        ||      |  | ||  || |||  ||||||  |||  | ||| || || |||   |  || |   ||   |    ||  ||||| ||||||||| |   ||||  ||||||||||||| || ||||||||||| || ||  ||||||| |||||| | |||||||| || || || |||||
-------gtgagcagcaactctgg-tcttta--ctattgtttttttagtttgtaaatatatgctacactcaa--aaccatcatgttacagGTCGGCATCTTTGCACTCTACCCGTGGACCCAAATATTGGAAAGATGCTTCTGATTGGAGCTATCTTCCAGTGCGTCAATCCTGCTTTGACAATCGCTGC

upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 12
gtatattatgctggatatgtttgtctccttaagctattgagtttagatttttagatctatctgaggctgagctaattttatacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTCTCATGGGCTCTATCTTTCAGTGCTTAAATCCTGCCTTAACTATTGCTGC
||||   |   ||||| | | ||  | || |   |  ||  |||| | | |||    | | |  ||   |              |  ||| |  ||||| || ||  |||||||||| |||||||| || |||||||| |||||||| || |||||||||||| | || ||||| ||||| ||||| ||
gtatgcaagattggatttttgtgatttct-agctttatgcctttataatcttaccctttttttgggtgaa--------------tacagGCCGCCATCTCTGCAAATTACCTTTGGATCCAAATATTGGAAAGATGCTCCTCATGGGGTCCATCTTTCAGTGCCTTAACCCTGCATTAACAATTGCAGC
















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|7285105|gb|AW597592.1|AW597592
EST:     TCTCAAAACAATTGGGGCGTTAGATGAACAGGAAGAGCTCACTCCACTTG                         GTCAGCATCTTTGTAACATACCTTTGGACCCAAATATANGGAAGATGCTTC
genomic: TCTCAAAACAATTGGGGCGTTAGATGAACAGGAAGAGCTCACTCCACTTGgtatattatg ... atacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTC
EST: gi|209729559|gb|BW655148.1|BW655148
EST:     TCTCAAAACAATTGGGGCGTTAGATGAACAGGAAGAGCTCACTCCACTTG                         GTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTC
genomic: TCTCAAAACAATTGGGGCGTTAGATGAACAGGAAGAGCTCACTCCACTTGgtatattatg ... atacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgagtttagatttttagatctatctgaggctgagctaattttatacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTCTCATGGGCTCTATCTTTCAGTGCTTAAATCCTGCCTTAACTATTGCTGC
                                   agctaat  putative branch site (score: 3)
                                      taattttatacttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattatgctggatatgtttgtctccttaagctattgagtttagatttttagatctatctgaggctgagctaattttatacttgtagGTCAGCATCTTTGTAACATACCTTTGGACCCAAATATAGGGAAGATGCTTCTCATGGGCTCTATCTTTCAGTGCTTAAATCCTGCCTTAACTATTGCTGC

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