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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatattttttgatgtcattatcatattagtataccgtgctttgttttatcttatgaccctgttcatttgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC

Basic information

species Glycine max
transcript GLYMA07G36550.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 10
gtattatattttttgatgtcattatcatattagtataccgtgctttgttttatcttatgaccctgttcatttgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC
||| | |||    | |    || | |   ||| | |  | |  |   | || |  || ||||   ||  |||    | ||  | |||  |||| ||| ||||  ||| | || || ||||| ||||||||| | ||||| ||||||||||| ||||| || ||||| ||||||||
gtaat-tatcaaataactgaataagccacttattgttgcata-tccatcttttggtaagaccaccttgctttactgtgatcac-agGCTGGTTGTTTGTGGTACGAGTACATTTATAAGCTAGACAAGATTACCTACAACAAATACCATCCCTATACATCCTGGATCCCCATAAC

upper sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G06550.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattata-----ttttttgatgtcatt----atcatattagtataccgtgctttgttttatcttatgaccc-tgttcatt-tgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC
|||||| |     |  |||||  |  ||     | | |  ||  |   |    ||||| |  |   | | |  | ||  || | |   || || |||||||| ||||| ||||  ||| ||||||||||| |||||||| |  | ||||| ||||| |||||||| ||||| |||||||| |||||
gtattacaagtcatcatttgactttctttcaggtgaaagaagcctcttgcatattgttcttccagctaatctatctttgttattatgaaacttttagGTGGGATATTTTTGGTACGAGTATATATACAAGATGGACAAGTTAACTTACAACAAATATCATCCTTACACCTCTTGGATTCCAATAAC

upper sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 10
gtattatat-tttttgatgtcattatcatattagtataccgtgctttgttttatcttatgaccctgttcatttgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC
||||||||  ||  | | | | ||   |  ||  |  |   | |  ||| | ||   |  | ||| ||      |   ||||   ||||||| ||| | ||||| |||||||||||||||||||||||| || |||||||||| |||||||| ||||||||||||||||| |||| 
gtattataaattccttaggacgtt-caacttttctcaaaattcccatgtctgatgcaaacagcctttt------atgaaattcacagGTGGGATATCTGTGGTTCGAGCATATATACAAGCTGGACAAGCTTACATACAATAAGTACCATCCATATACCTCATGGATTCCAATAAG

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|193660971|gb|FK602163.1|FK602163
EST:     TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTG                         GTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCAT
genomic: TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTGgtattatatt ... taatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCAT
EST: gi|193513713|gb|FK467327.1|FK467327
EST:     TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTG                         GTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATA
genomic: TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTGgtattatatt ... taatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATA
EST: gi|17519074|gb|BM188116.1|BM188116
EST:     TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTG                         GTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATAC
genomic: TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTGgtattatatt ... taatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATAC
EST: gi|193387768|gb|FK350973.1|FK350973
EST:     TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTG                         GTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATAC
genomic: TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTGgtattatatt ... taatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATAC
EST: gi|193726520|gb|FK656180.1|FK656180
EST:     TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTG                         GTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGNTTGCAT
genomic: TCAAGCGCAGAATATCAATCAAAGCAACTGTTGTGCTGATATGTTCATTGgtattatatt ... taatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtataccgtgctttgttttatcttatgaccctgttcatttgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC
                                          acttaat  putative branch site (score: 4)
                                                tttct  CT-rich tract
            tttgttttatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatattttttgatgtcattatcatattagtataccgtgctttgttttatcttatgaccctgttcatttgacttaatttctagGTGGGTTATTTATGGTTTGAGCATATATACAAGCTGGACAAGATTGCATACAATAAATACCATCCTTATACCTCATGGATTCCCATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA