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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacactgactctcacgtatagtttcagtttgttctgaatttcaagttttgatttgactctttccacataacttgtgatattcatttctgggaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAATTGTTAAGAAGCAGACTGCCCTGAAG

Basic information

species Glycine max
transcript GLYMA06G14590.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G14590.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 1
cacactgactctcacgtatagtttcagtttgtt-ctgaatttcaagttttgatt---tgactctttccacataac--ttgtgatattcatttctgggaa------cttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAATTGTTAAGAAGCAGACTGCCCTGAAG
             || ||||  | ||  ||     || || || | ||||| ||     |   || |||  |||   ||   |||  || |   || |         |||||||||||||||||||||||| ||  | ||||| ||||||||||||||||| ||  |   |||||| |||||  |||||
------------aacatataaatccatctttcaattgcatatctatttttgcttgtgcaatgattgccatgtaagcatttcaatacacactaaaggaagggttgttgtgcagGTTTCTTTGTCACAATTTGGATTGCTGCTGTAATGTTCAAGTCAAATGATATATTGCGGAAGCAAACTGCTTTGAAG
















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|9819498|gb|BE555011.1|BE555011
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|208123385|gb|GD921361.1|GD921361
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|207807586|gb|GD776605.1|GD776605
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|208049865|gb|GD844024.1|GD844024
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|208144909|gb|GD943472.1|GD943472
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|193671945|gb|FK616271.1|FK616271
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAGCATTTGCAAG                         GTTTCTTTGTCACAATTTGTATGTCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|193557168|gb|FK512811.1|FK512811
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
EST: gi|9819411|gb|BE554924.1|BE554924
EST:     ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAG                         GTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA
genomic: ACCGTTTTCTCTCTTGTTGCTGATTGTTTTCATCCGCCAACATTTGCAAGgtactgcttc ... gaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgatttgactctttccacataacttgtgatattcatttctgggaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAATTGTTAAGAAGCAGACTGCCCTGAAG
                   acataac  putative branch site (score: 3)
                               atattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacactgactctcacgtatagtttcagtttgttctgaatttcaagttttgatttgactctttccacataacttgtgatattcatttctgggaacttgcagGTTTCTTTGTCACAATTTGTATATCAGCTGTGATGTTCAAGTCAAATGAAATTGTTAAGAAGCAGACTGCCCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
cacactg
- - - - ctctcac
- - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctgg