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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaaatatttcattaatttttgtgatattgggtggttatctatttctctggttactgcctgattattcttgtctacctcacctaattgtgtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCAGAGCTGGTTTGTATATACAACGAGCTTCGTGAAATTGGAAAGGCACCAC

Basic information

species Glycine max
transcript GLYMA03G40000.2
intron # 4
splice site 3'
intron type U2

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|298180727|gb|HO022166.1|HO022166
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
EST: gi|213615160|gb|DB964968.1|DB964968
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
EST: gi|192301788|gb|FG997674.1|FG997674
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
EST: gi|213614510|gb|DB969115.1|DB969115
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
EST: gi|46492660|gb|CN472216.1|CN472216
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
EST: gi|298170197|gb|HO018821.1|HO018821
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGCTGGGTTTGGCA
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCA
EST: gi|151396136|gb|EV266013.1|EV266013
EST:     TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTG                         CCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTTGGGTTTTGG
genomic: TGAAGAAAGGAAAGCACTTCATTCTGATAAGAAATCCTCTTGATATATTGgtaaaatgtc ... gtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTT-GGGTTT-GG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctggttactgcctgattattcttgtctacctcacctaattgtgtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCAGAGCTGGTTTGTATATACAACGAGCTTCGTGAAATTGGAAAGGCACCAC
                                   acctaat  putative branch site (score: 3)
                 attattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaaatatttcattaatttttgtgatattgggtggttatctatttctctggttactgcctgattattcttgtctacctcacctaattgtgtatgtccagCCATCCTTTGATAAGGTTGTCCCTCCATCTTTCTATGAGTTGGGTTTGGCAGAGCTGGTTTGTATATACAACGAGCTTCGTGAAATTGGAAAGGCACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT