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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttctaacagtggaaatggcttgaaaacagtttcaactctaatcatggtattctatctggttcgagggcacattctttttaacttttgtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAGACCACCCTAGTTGCATTACAAGATATAACTTTAGAGAAAATATTTGATG

Basic information

species Glycine max
transcript GLYMA08G21610.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 17
lower sequence: AC187157.4_FGT005 (Zea mays), 3'ss of exon 16
----tttgttctaacagtggaaatggcttgaaaacagtttcaactctaatcatggtattctatctggttcgagggcacattctttttaacttttgtt--tatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAGACCACCCTAGTTGCATTACAAGATATAACTTTAGAGAAAATATTTGATG
      || ||||         ||   |  |||||  |   | ||       ||| |  ||  |  ||  | |    ||   |    |      |||   | |||||| |||||||||||||| ||| |||||||| ||||||| |||||||| ||||| || || || ||  | || || ||  |  | |||| | | || || |
gttcgctgctctattgcattgcatcattctaaaacgttgctagcttgtggagtgggaa-ctggcaagtgagggctgccacggtgacgactcgacgttcccacgcagGCCTTGCCAGTGTTCACGTTCGCGAACCAGTCCGGGCTCGACATGCTGGAGACGACGCTGGTGGCGCTGCAGGACATCGCGCTGGAGAGAGTGTTCGACG
















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|209723191|gb|BW675137.1|BW675137
EST:     TCAAGTCCTTGTGGCATCACTCTGATGCAATATTGTGCTGCACTCTAAAG                         GCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
genomic: TCAAGTCCTTGTGGCATCACTCTGATGCAATATTGTGCTGCACTCTAAAGgtatgcttga ... gtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
EST: gi|6746945|gb|AW317401.1|AW317401
EST:     TCAAGTCCTT-TGGCATCACTCTGATGCAATATTGTGCTGCACTCTAAAG                         GCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
genomic: TCAAGTCCTTGTGGCATCACTCTGATGCAATATTGTGCTGCACTCTAAAGgtatgcttga ... gtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
EST: gi|193624440|gb|FK574320.1|FK574320
EST:     AATATTGTGCTGCACTCTAAAG                         GCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
genomic: AATATTGTGCTGCACTCTAAAGgtatgcttga ... gtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
EST: gi|58017273|gb|CX704015.1|CX704015
EST:     TCAAGTCCTTGTGGCATCACTCTGATGCAATATTGTGCTGCACTCTAAAG                         GCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG
genomic: TCAAGTCCTTGTGGCATCACTCTGATGCAATATTGTGCTGCACTCTAAAGgtatgcttga ... gtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatggtattctatctggttcgagggcacattctttttaacttttgtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAGACCACCCTAGTTGCATTACAAGATATAACTTTAGAGAAAATATTTGATG
                                  ttttaac  putative branch site (score: 2)
                                        cttttgttt  CT-rich tract
                             attctttttaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttctaacagtggaaatggcttgaaaacagtttcaactctaatcatggtattctatctggttcgagggcacattctttttaacttttgtttatgcagGCATTGCCAGTGTTCACTTTCTCGAACCAGGCCGGGCTTGACATGCTAGAGACCACCCTAGTTGCATTACAAGATATAACTTTAGAGAAAATATTTGATG

- - - - - - - - - -tggcttg
- - - - - - - - - - - - - - - - - - caactct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtt