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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctttcttatctttaataatattatatttgtacttttatcaaatgaaagcataaaaggggcatttacaaatatactggattctaccaatcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCAAGTCCAGGATTTACAAAG

Basic information

species Glycine max
transcript GLYMA10G31310.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------ctttctttcttatctttaataatattatatttgtacttttatcaaatgaaagcataaaaggggcatttacaaatatactggattctaccaatcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCAAGTCCAGGATTTACAAAG
                             |||  | | | | ||    | | ||||| ||| |  | || ||||||   | || | ||     |||   |||||      |   || ||    ||| |||||||| ||||| || | || |||||||| ||||| |||||||| |||||||||||||| || || |||
gtgagttcaatcagaattttaaaatgtagcttcttgtgtaacctcc--tgagattatgtttctg-tcttgtcaaatttca-cacacaaa----attccaaaatacctaacacgttatcatgtattttagGCTTTCCTGAAATATGTGGACTTCAATGTTGTTCGCTGTGCTGTCATTGCAAGTCCAGGTTTCACCAAG
















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|193650755|gb|FK595878.1|FK595878
EST:     GC-TTGGATAAGTTC-TTCAGAATG-TTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
EST: gi|9898819|gb|BE607787.1|BE607787
EST:     GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
EST: gi|208083199|gb|GD879229.1|GD879229
EST:     GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAG                         GCTTTCTTGAAACATATAGATTTCAA
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAA
EST: gi|193472093|gb|FK437096.1|FK437096
EST:     GCTTTGGATAAGTTCTTTCAGAATG-TTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
EST: gi|208087721|gb|GD888581.1|GD888581
EST:     GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTT
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTT
EST: gi|193483997|gb|FK451966.1|FK451966
EST:     GGATAAGTTCTTTCAGAATG-TTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
genomic: GGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
EST: gi|23731912|gb|BU764103.1|BU764103
EST:     GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCA
EST: gi|208119461|gb|GD917394.1|GD917394
EST:     GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAG                         GCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAA
genomic: GCTTTGGATAAGTTCTTTCAGAATGTTTTGCAGgtaatttcag ... atcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaagcataaaaggggcatttacaaatatactggattctaccaatcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCAAGTCCAGGATTTACAAAG
                                              tcttttc  CT-rich tract
                   atttacaaatatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttctttcttatctttaataatattatatttgtacttttatcaaatgaaagcataaaaggggcatttacaaatatactggattctaccaatcttttcagGCTTTCTTGAAACATATAGATTTCAATGTGGTTCGTTGTGCTGTAATTGCAAGTCCAGGATTTACAAAG

- - - - - - - - - - - - - - - - - - - - - -aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atactgg