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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAATTCAAGATCCATGCCTCAAATCTTCCATTCCTCACTTTCCCCCTGTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAGgttagtgtatagacttgaaattcattggtggttatattattttttacttgattgaaggaaactacttaaggtttcaattatatacatataagatgttttt...

Basic information

species Glycine max
transcript GLYMA19G05450.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G05450.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G406177_T01 (Zea mays), 5'ss of exon 8
---TCAAAATTCAAGATCCATGCCTCAAATCTTCCATTCCTCACTTTCCCCCTGTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAGgtt-agtgtatagacttgaaattcattgg---tggttatattattttttacttgattgaagg-aaactacttaaggtttcaattatatacatataagatgttttt
   |        || |   | |     || |   |||  |||   | || |   |    ||  | |||||||| |||||||| ||||||||||||  ||||||||| | | | |    |      |  ||     |       |||||  |  ||| | ||   | | | |    |  | || | ||| ||    | |  |       
AAATTGTCGCCAAAAAATTAAGTGCAGAAAC---CATATCTCTACTACCTCAGATTGTACTATTGCATGGAACAGCAGATTACTCCATACCATCATCTGCCAGgttcattatttttgttctgggctagtttactctaaccgggttattgataccttaagtgtttgcatattttccactgctttatttagatgtcaacatcaat-----
















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|51343614|gb|CO984347.1|CO984347
EST:     GTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAG                         TGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
genomic: GTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAGgttagtgtat ... atttttgtagTGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
EST: gi|10253108|gb|BE820874.1|BE820874
EST:     GAACTGCAGATTATTCCATACCATCAGTTGCCAG                         TGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
genomic: GAACTGCAGATTATTCCATACCATCAGTTGCCAGgttagtgtat ... atttttgtagTGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
EST: gi|7028541|gb|AW458324.1|AW458324
EST:     TCCATACCATCAGTTGCCAG                         TGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
genomic: TCCATACCATCAGTTGCCAGgttagtgtat ... atttttgtagTGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
EST: gi|9903021|gb|BE611989.1|BE611989
EST:     GTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAG                         TGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
genomic: GTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAGgttagtgtat ... atttttgtagTGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT
EST: gi|31462722|gb|CD404750.1|CD404750
EST:     GTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAG                         TGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGATTTGAT
genomic: GTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAGgttagtgtat ... atttttgtagTGAGCGGTTTGCGGAAGCTCTTAAGAAGGCAGGGGTAAGAGCTGAGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAATTCAAGATCCATGCCTCAAATCTTCCATTCCTCACTTTCCCCCTGTATATCTGGTCCATGGAACTGCAGATTATTCCATACCATCAGTTGCCAGgttagtgtatagacttgaaattcattggtggttatattattttttacttgattgaaggaaactacttaaggtttcaattatatacatataagatgttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggtgg