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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttagatagcagttgattattacttgtggaattatataatatggttggttagttaaatttgttattctattttgtcttatcgccctctttggttttttgttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCCAAAAGGAGAATTTTGCCACAATATGCT

Basic information

species Glycine max
transcript GLYMA09G04910.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ17196 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtgtttagatagcagttgattattacttgtggaattatataatatggttggttagttaaatttgt-tattctattttgtcttatcgccctctttggttttttgttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCCAAAAGGAGAATTTTGCCACAATATGCT
                                                                   || | ||| |||||   | |      |  ||    |    |    |||||||  || ||||||||||| ||||| ||||||||||| ||||||| | | || |  || || |||   ||||| |||||
-------------------------------------------------------------------gtatgttcgatttttcttaagtatgtttgtttcactaacttgccttgcagGCCCGCGTTTGCATCTGCCTCAGCGGACAATATTAAGAAGTTCAGCTTGCCGAGGGGCGAGTTTGTGCACAACATGCT

upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31158 (Selaginella moellendorffii), 3'ss of exon 14
gtatgtgtttagatagcagttgattattacttgtggaattatataatatggttggttagttaaatttgttattctattttgtcttatcgccctctttggttttttgttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCCAAAAGGAGAATTTTGCCACAATATGCT
                                                                                    ||| |     ||   |   |||     |||||||  || ||||||||||| ||||| ||||||||||| ||||||| | | || |  || || |||   ||||| |||||
-----------------------------------------------------------------------------------gtat-gtttgtttcactaacttgcc--ttgcagGCCCGCGTTTGCATCTGCCTCAGCGGACAATATTAAGAAGTTCAGCTTGCCGAGGGGCGAGTTTGTGCACAACATGCT
















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|58021862|gb|CX708603.1|CX708603
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|208133389|gb|GD929096.1|GD929096
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|193634880|gb|FK583941.1|FK583941
EST:     TACAAACCAATAAAAAATACTGTTCGAGCAATGGCCCAGCATCCCAGAGA                         GCAAGCTTTTGCATCTGCTTCAGCTGACAATATT-AAAAGTTCACCCTTCC
genomic: TACAAACC-ATAAAAAAT-CTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|21888738|gb|BQ741951.1|BQ741951
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAATA                         GTAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|10236381|gb|BE805269.1|BE805269
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAAGCCTTTGCATCGTGCTTCAGCTGACAATATTAAAAAGTTCACCCTT
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAA-GCTTTTGCATC-TGCTTCAGCTGACAATATTAAAAAGTTCACCCTT
EST: gi|193460952|gb|FK426699.1|FK426699
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|254313963|gb|GR831592.1|GR831592
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCAACCTTCC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|208324693|gb|GE125770.1|GE125770
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCC
EST: gi|207777106|gb|GD747893.1|GD747893
EST:     CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGA                         GCAAGCTTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTC
genomic: CTTACAAACCATAAAAAATCTGTTCGAGCAATGGCCCAGCATCCCAAAGAgtatgtgttt ... ttggctgcagGCAAGC-TTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttgttattctattttgtcttatcgccctctttggttttttgttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCCAAAAGGAGAATTTTGCCACAATATGCT
                                      ttttttgtt  CT-rich tract
     tgttattctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtttagatagcagttgattattacttgtggaattatataatatggttggttagttaaatttgttattctattttgtcttatcgccctctttggttttttgttggctgcagGCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCCAAAAGGAGAATTTTGCCACAATATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA