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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaaatttcttttaaacccccacccagcccctttctttcatgagtatactgtatttcctttgggtgcaatagttaattctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT

Basic information

species Glycine max
transcript GLYMA16G34660.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G34660.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
cttaaatttcttttaaacccccacccagcccctttctttcatgagtatactgtatttcctttgggtgcaatagttaattctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT
       |  ||||   |        |   |  |||| |||||    |  ||| |||  ||      |    | ||||       ||||  ||  |||||||  ||||||| |||||||| |||||||||||||| |||||  |  | ||||||  ||    |||| | || | |||| |  | ||| | |||||| |  
------gtaatttttccctttttgatatttctcttctctcatgta-gtgttgtgtttgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC

upper sequence: GLYMA16G34660.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
--cttaa--atttcttttaaacccccacccagcccctttctttcatgagtata-ctgtatttcctttgggtgcaatagttaatt-ctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT
  ||| |  | ||  | |  |   | |         ||| | |  |||||  |  ||||     |||   | ||||  | | |   |  |||| ||| ||  |||||| ||||||||||| ||||||||||||||||||||||||||  |||||||||||   || |||||  | || | |  | |||| ||| | |||||  || 
tgcttgaggaattgctcttcattgcaatttga----tttatctggtgagttcagttgtacaatatttt--tccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA
















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|298165084|gb|HO011133.1|HO011133
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|192302694|gb|FG993714.1|FG993714
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|22524321|gb|BU083132.1|BU083132
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|21676111|gb|BQ628462.1|BQ628462
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         CTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|6072588|gb|AW101975.1|AW101975
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|20813952|gb|BQ298430.1|BQ298430
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|19934415|gb|BQ079445.1|BQ079445
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|22524199|gb|BU083010.1|BU083010
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|22524381|gb|BU083192.1|BU083192
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|23732021|gb|BU764165.1|BU764165
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|151400455|gb|EV270269.1|EV270269
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|192302695|gb|FG993715.1|FG993715
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
EST: gi|15337017|gb|BI497673.1|BI497673
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGTATTGT
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTG-ATTGC
EST: gi|151400687|gb|EV270501.1|EV270501
EST:     AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATT                         GTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA
genomic: AAGAATCTTGGGACCAAAAGTTGGATCAAGCGAGGAAGGAGAGTAAAATTgtaagtttta ... tttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactgtatttcctttgggtgcaatagttaattctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT
                                ttctaaa  putative branch site (score: 2)
                                        cttcattttt  CT-rich tract
                       aatagttaattctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaaatttcttttaaacccccacccagcccctttctttcatgagtatactgtatttcctttgggtgcaatagttaattctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT

- - - - - - - - - ccccacc
- - - - - - - - - - - - - - ccccttt
- - - - - - - - - - - - - - - - - - - tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcttca