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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttgtattaactgctgattttttcttcaaagtcacggtttaagccttgcacaatttctgtcttcctgatgtcatcttcattcttgtttttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT

Basic information

species Glycine max
transcript GLYMA15G40590.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40590.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G872417_T01 (Zea mays), 3'ss of exon 4
---actttgtattaactgctgattttttcttcaaagtc-acggtttaagccttgcacaatttctgtcttcctgatgtcatcttcattcttgtttttaact-acagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT
       || ||      ||    | ||||  ||  ||  | ||| |     ||   | ||     |    |    || |  | ||     |  || |||  ||||| || || |||||||||||||||||| | ||||| |||||||||||||||||
tgcgtactgcatgtggcactatcatattctctaatttctgctgttca-----tgagaatttggcagcacatttggatccttatgataaacatgattgacttgcagGAGGGAGTCCAACAACTTGTTCTTGGTCTGTACATTATCAGGGGTGACAACAT
















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|22927651|gb|BU544790.1|BU544790
EST:     CCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|192300038|gb|FG992191.1|FG992191
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTTTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|193496721|gb|FK460305.1|FK460305
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACATGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|208303248|gb|GE101069.1|GE101069
EST:     CTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|151399825|gb|EV269696.1|EV269696
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|298199205|gb|HO042568.1|HO042568
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|192300037|gb|FG992190.1|FG992190
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|7285928|gb|AW598415.1|AW598415
EST:     CATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|151395293|gb|EV265164.1|EV265164
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|192310890|gb|FG998894.1|FG998894
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
EST: gi|192310889|gb|FG998893.1|FG998893
EST:     CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAG                         GAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC
genomic: CAACAAATATAATTCTTGATGAGTCCCATGAACGAGTTTATTCTACCAAGgtatgatgaa ... ttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgcacaatttctgtcttcctgatgtcatcttcattcttgtttttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT
                                           ttttaac  putative branch site (score: 2)
                              tcttcattcttgtttt  CT-rich tract
                                   attcttgtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttgtattaactgctgattttttcttcaaagtcacggtttaagccttgcacaatttctgtcttcctgatgtcatcttcattcttgtttttaactacagGAAGGTGTACAACAACTTGTTCTTGGTTTATACATCATCAGGGGTGACAACAT

- - - - - - ctgctga
- - - - - - - - - - - - - - - - - - - - - - -ccttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc