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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctatcatattatatttgacattcctaattaatcgttggagatttggagctaacaagttgtcaatgctgaactttacatccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGATCTTGGCCTTTATGTATTTGCTTCCAAGCCATCAAGTGGTGCTGCTATCT

Basic information

species Glycine max
transcript GLYMA17G03990.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 12
gtttgctatca--tattatatttgacattcctaattaatcgttggagatttggagctaacaagttgtcaatgctgaactttacatccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGATCTTGGCCTTTATGTATTTGCTTCCAAGCCATCAAGTGGTGCTGCTATCT
|| || |  |   |   | |  ||  |||||    |     ||  | |        |   |  ||    ||  |||  |  |         |||||    |||||||| || || || || |||||||| || || ||||| || |||||||| ||| |||| ||||| |||||||| ||||||||||| ||||
gtctgtttcctactcccaaagctggaattccactctctctcttacaaaagcaagtttttgacattagacatcatga-ttccatgcttttatcagGATCAATTCTACCAATCAAGGATTGAGAAGGGCGTGATCAACAAGAATGACCTTGGCCTGTATATATTCGCTTCAAAGCCATCTAGTGGTGCTGCCATCT
















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|207764390|gb|GD736763.1|GD736763
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|214007370|gb|DB986250.1|DB986250
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|213606347|gb|DB976508.1|DB976508
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|7926145|gb|AW832171.1|AW832171
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|254317534|gb|GR826518.1|GR826518
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|14205721|gb|BG839399.1|BG839399
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|41145398|gb|CK605609.1|CK605609
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|14205748|gb|BG839426.1|BG839426
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|58019629|gb|CX706371.1|CX706371
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|21601505|gb|BQ611836.1|BQ611836
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATTCTT-ATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|26048836|gb|CA785289.1|CA785289
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|209712398|gb|BW671250.1|BW671250
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|254317533|gb|GR826517.1|GR826517
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|58019308|gb|CX706050.1|CX706050
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|208168633|gb|GD968707.1|GD968707
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACTAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|6747837|gb|AW318293.1|AW318293
EST:     AGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: AGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|13789489|gb|BG652080.1|BG652080
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|209699971|gb|BW661200.1|BW661200
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgctatc ... tccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttggagatttggagctaacaagttgtcaatgctgaactttacatccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGATCTTGGCCTTTATGTATTTGCTTCCAAGCCATCAAGTGGTGCTGCTATCT
              agctaac  putative branch site (score: 2)
                                    aacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctatcatattatatttgacattcctaattaatcgttggagatttggagctaacaagttgtcaatgctgaactttacatccaatgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGATCTTGGCCTTTATGTATTTGCTTCCAAGCCATCAAGTGGTGCTGCTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT