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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattttaaaaataaaagcactattgtgttgtacagaagacttcttttctttactcttggttgatcctttgcttatcaatcatctttatgttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATTTTGGCAGAAAACAAACATGTACAACAATCCTGATACCTTTATTAATGGC

Basic information

species Glycine max
transcript GLYMA12G09200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0061g01530.t01 (Vitis vinifera), 3'ss of exon 4
------ctattttaaaaataaaagcactattgtgttgtacagaagacttcttttctttactcttggttgatcctttgcttatcaatcatctttatgttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATTTTGGCAGAAAACAAACATGTACAACAATCCTGA-TACCTTTATTAATGGC--
        ||||| |  || | |   |       ||||         |  ||||||  | |  |||  ||   || | | ||  ||    ||||||       | ||||||  ||||||| |||||||||||||| | ||||||| | || | |||||||||||| ||||  ||| |     | || |   |     |   |||     
atttactaatttttatgatcaga-ttcccccaaattgtgtgat---ttggttttctagaataatggaggacttttagttgat--attcagtttatgcaaa---tggcagGTTCTGGATTTACTTGAAGATGCTTGTGAATCATTATTAGACAGCATTTTGGCAGAGAACAGTCATCTTTTGGATTCTTAGCTGTGGCTGCAAATTTAAT
















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|192316065|gb|FK008890.1|FK008890
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAG                         --G-TGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|7639199|gb|AW733527.1|AW733527
EST:     GGACCACAAGGGTTTGAG-A-                         -AGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: GGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|192332259|gb|FK023908.1|FK023908
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAT                         --G-TGTTGGATTTGCTTGA-GATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|192298963|gb|FG987708.1|FG987708
EST:     CTTATTATGGTGGACCACAAGGGTTTGAG-A-                         -AGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: CTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|27424689|gb|CA936209.1|CA936209
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAG                         --G-TGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|207692884|gb|GD675473.1|GD675473
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAG                         --G-TGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|213602386|gb|DB980449.1|DB980449
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAG-A-                         -AGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|33388402|gb|CA851609.1|CA851609
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCGCAAGGGTTTGAGAAG                         CAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCAT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCAT
EST: gi|192332260|gb|FK023909.1|FK023909
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAG                         --G-TGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
EST: gi|24205701|gb|BU964954.1|BU964954
EST:     AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAG                         --G-TGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT
genomic: AAAGTGAAGTTCCGGATCCTTATTATGGTGGACCACAAGGGTTTGAGAAGgtatgctatt ... ttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttactcttggttgatcctttgcttatcaatcatctttatgttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATTTTGGCAGAAAACAAACATGTACAACAATCCTGATACCTTTATTAATGGC
             ggttgat  putative branch site (score: 5)
                           ttatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattttaaaaataaaagcactattgtgttgtacagaagacttcttttctttactcttggttgatcctttgcttatcaatcatctttatgttggcactagCAGGTGTTGGATTTGCTTGAAGATGCTTGCGGATCATTACTGGAAACCATTTTGGCAGAAAACAAACATGTACAACAATCCTGATACCTTTATTAATGGC

- - - - aaaataa
- - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttgc