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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaattcagttagttttaatatccttggatgttattgttgatggtaatgttgtttacgaagctgattgattttgaattctgaattttggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGCTGAACACTTCTGCCTACTTTTTTAAGAAAACCGCTGATCTCATTGATTT

Basic information

species Glycine max
transcript GLYMA18G49660.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 1
-attttaattcagttagttttaatatccttggatgttattgttgatggtaatgttgtttacgaagctgattgattttgaattctgaattttggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGCTGAACACTTCTGCCTACTTTTTTAAGAAAACCGCTGATCTCATTGATTT
 | |||     | ||  |       || ||  |  |   | ||| |  | || || |||  |  | |      |     ||  ||  ||| |     |||| ||||||| | ||| | || || |  ||||||| |||||| ||||| ||| | || |||||||| |||||||| |||||||| ||||| |||||||||||
gaatttggcatatttgttaagcccttctttttacatgcatcttgtttattat-ttattttgggggttagccactcagtgatgttgcctttggtttgagcagGTGAAAGATTAGGTCGCGGCATAGTTACTGATGCAATTACTACCCCAGTGGTCAATACTTCTGCTTACTTTTTCAAGAAAACTGCTGAGCTCATTGATTT
















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|6502087|gb|AW203460.1|AW203460
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGGAATTACCACCCCTGTG
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGG-AATTACCACCCCTGTG
EST: gi|7924308|gb|AW830334.1|AW830334
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|209720777|gb|BW677377.1|BW677377
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCT
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCT
EST: gi|254343496|gb|GR857252.1|GR857252
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|209713258|gb|BW684345.1|BW684345
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|209701006|gb|BW652144.1|BW652144
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|213588426|gb|DB959746.1|DB959746
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTAC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTAC
EST: gi|13791349|gb|BG653940.1|BG653940
EST:     ATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: ATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|254314402|gb|GR831987.1|GR831987
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|4290040|gb|AI438012.1|AI438012
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGC
EST: gi|209720940|gb|BW682419.1|BW682419
EST:     AGTTCTTATTCANTTTTNGAAATC-GATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCA
genomic: AGTTCTTATTCATTTTT-GAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCA
EST: gi|20075818|gb|BQ094601.1|BQ094601
EST:     TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCG                         CTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACC
genomic: TAGTTCTTATTCATTTTTGAAATCCGATGCAAGCAAAACGATTCATGCCGgtacgtaaaa ... ggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaatgttgtttacgaagctgattgattttgaattctgaattttggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGCTGAACACTTCTGCCTACTTTTTTAAGAAAACCGCTGATCTCATTGATTT
                     gattgat  putative branch site (score: 4)
                      attgattttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaattcagttagttttaatatccttggatgttattgttgatggtaatgttgtttacgaagctgattgattttgaattctgaattttggcaatgcagCTGAAAGACTGGGTAGGGGTATTGAGACTGATGGAATTACCACCCCTGTGCTGAACACTTCTGCCTACTTTTTTAAGAAAACCGCTGATCTCATTGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - -ccttgga
- - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattc