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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttaacttctctctctttttttttttttaatctttactcttgtttatctcatcttttcattcattcattcattcattgtttcatttattcagGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACATCGCCCAGGCTTTGCATTATTGCAGCTCTGAGGGTCGTCCCTTGTACCA

Basic information

species Glycine max
transcript GLYMA14G00540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35230.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------------------gtatgtttaacttctctctctttttttttttt--taatctttactcttgtttatctcatcttttcattcattcattcattcattgtttcatttattca--gGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACATCGCCCAGGCTTTGCATTATTGCAGCTCTGAGGGTCGTCCCTTGTACCA
                                                                                          ||||||  |    |          |  |||   | |  | || | |  |  |       ||||  ||  || ||    |  ||||||   |||||||  ||||||| |||||| ||||||||||||||| |||||||||| |    |||||| ||  |||||||| ||||||| ||  ||||||||||||| ||||||||
gtatgctttttctccttcttttattgcctcttgtctaaagctgggaactttagtaatgtttgctgatattaggagcttgcatttatggtttatgttagatggatgaaaagagactactttaggtgaattataatgtcttaaaaggtgaatttttgtttctt-atcttgttgttgttttggttattcacagGGGAAAATCAGACAATTGAGTGGGCTATGAGGTTGCGAGTAGGATATTACATAGCTGAGGCTTTGGATTATTGTAGTACTGAGGGTCGTCCATTGTACCA
















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|193536309|gb|FK489605.1|FK489605
EST:     CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACT                         GGGAAACTCAGAACTATTGAGTGG
genomic: CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACTgtatgtttaa ... atttattcagGGGAAACTCAGA-CTATTGAGTGG
EST: gi|16349103|gb|BI974698.1|BI974698
EST:     CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACT                         GGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCT
genomic: CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACTgtatgtttaa ... atttattcagGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCT
EST: gi|16349558|gb|BI975153.1|BI975153
EST:     CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACT                         GGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACA
genomic: CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACTgtatgtttaa ... atttattcagGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACA
EST: gi|213606190|gb|DB961334.1|DB961334
EST:     CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACT                         GGGAAACTCAGACTATTGAGTGGGCCATGCGGTTGCGAGTCGCTCTTTACA
genomic: CGTTGCCGAGTACATGCCTAATGATACTCTTGCCAAGCATCTTTTCCACTgtatgtttaa ... atttattcagGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtttatctcatcttttcattcattcattcattcattgtttcatttattcagGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACATCGCCCAGGCTTTGCATTATTGCAGCTCTGAGGGTCGTCCCTTGTACCA
                                         tttcattt  CT-rich tract
                                     attgtttcatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttaacttctctctctttttttttttttaatctttactcttgtttatctcatcttttcattcattcattcattcattgtttcatttattcagGGGAAACTCAGACTATTGAGTGGGCTATGCGGTTGCGAGTCGCTCTTTACATCGCCCAGGCTTTGCATTATTGCAGCTCTGAGGGTCGTCCCTTGTACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC