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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccctcactattttccatttatactctagtttttagtttttcattatagtaggttagtcattctaatatcattattggttgtttttcctttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGAACTTATTTCCACAACAACAGAAAAGAAATCTTGGACTAGACCACCAATT

Basic information

species Glycine max
transcript GLYMA17G16630.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G16630.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 10
--acccctcactattttccatttatactctagtttttagtttttcattatagtaggttagtcattctaatatcattattggttgtttttcctttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGAACTTATTTCCACAACAACAGAAAAGAAATCTTGGACTAGACCACCAATT
       |   || |||||  | ||| ||   | | || || ||  || | |  | ||  ||| ||      |||  ||      | |   ||  | | |||||| ||||||||||| |||||||| ||||| ||  ||||||||||| ||||  | || || ||||    ||| |||||||||||||| || ||||| || 
gtgagtttatataatttcccctcatattcatctctataattctt--ttgttggtgttttatcaatcattcggcatcttt-----ctctcttttactctttagGATAAGAAAATTCCCAGGGCAAACAGAGTCCACGCTAAGTGCAGAAATTGAGTTGATCTCAACAATGGGAGAGAAGAAATCTTGGACAAGGCCACCGATC
















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|254325028|gb|GR834453.1|GR834453
EST:     ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAA                         GATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
genomic: ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAAgtaagtatct ... ttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
EST: gi|254325029|gb|GR834454.1|GR834454
EST:     ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAA                         GATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
genomic: ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAAgtaagtatct ... ttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
EST: gi|193382059|gb|FK345746.1|FK345746
EST:     GCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAA                         GATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
genomic: GCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAAgtaagtatct ... ttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
EST: gi|37996956|gb|CF808545.1|CF808545
EST:     CATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAA                         GATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
genomic: CATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAAgtaagtatct ... ttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
EST: gi|254315557|gb|GR825366.1|GR825366
EST:     ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAA                         GATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
genomic: ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAAgtaagtatct ... ttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
EST: gi|19346229|gb|BM891109.1|BM891109
EST:     ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAA                         GATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA
genomic: ACATCTGGCCGAGCAAAATACAATGCTTCTATTGATTGTTTGGTTTGGAAgtaagtatct ... ttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtaggttagtcattctaatatcattattggttgtttttcctttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGAACTTATTTCCACAACAACAGAAAAGAAATCTTGGACTAGACCACCAATT
                ttctaat  putative branch site (score: 2)
                                  ttgtttttcctttatt  putative PPT
               attctaatatcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccctcactattttccatttatactctagtttttagtttttcattatagtaggttagtcattctaatatcattattggttgtttttcctttatttctagGATTAGAAAATTCCCTGGGCAAACCGAGTCAACCTTAAGTGCAGAAGTTGAACTTATTTCCACAACAACAGAAAAGAAATCTTGGACTAGACCACCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA