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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctattttcttttccactttatctatgcaccagtttagattttttctatgatggagctaggataaacatttcgttgttttggcaatcctttaactcttgtcttgtgcaaaacatttgattgattgataaaactataaattttcaatctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCAAAGTCTCAAAAGAAAACATTTGACGACTCTGATGAAGACTAAGTGCTGG

Basic information

species Glycine max
transcript GLYMA01G01390.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G01390.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv02s0109g00380.t01 (Vitis vinifera), 3'ss of exon 14
gtctattttcttttccactttatctatgcaccagtttagattttttctatgatggagctaggataaacatttcgttgttttggcaatcctttaactcttgtcttgtgcaaaacatttgattgattgataaaactataaattttcaatctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCAAAGTCTCAAAAGAAAACATTTGACGACTCTGATGAAGACTAAGTGCTGG
                                               ||||    |  || | | || |||||      |  |        | |   || | |||   ||     |   | ||||| ||| |  ||   |  |   || ||   |||||||||| || |||||||| |||||||  |||||| ||| |||||||||||||||  ||||||  || |||||||||||||||||||| | | ||||| 
----------------------------------------------gtatgtcaaa--tatgctcaatatttcaggccatgagtg-----ctgagcattattttgattaagctggt--gtggattg-taatatgatgcctcatgtctcaattgcagGAGTCCAAGCTATATGGGGCTCACTTCAGAGAAATTGCTGCTGATGCTCCAAAGTCCAAAAAGATCACTTTTGACGACTCTGATGAAGATTGAATGCTGT
















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|9983987|gb|BE658095.1|BE658095
EST:     AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|193327363|gb|FK293832.1|FK293832
EST:     ACACATGTAAAGAAAAAG                         GAGTCC-AAC-TTAT-GGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: ACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|208096077|gb|GD892485.1|GD892485
EST:     AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|16277496|gb|BI942413.1|BI942413
EST:     AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|193397874|gb|FK363768.1|FK363768
EST:     AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|193593828|gb|FK548422.1|FK548422
EST:     AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|9983884|gb|BE657992.1|BE657992
EST:     AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
EST: gi|58022098|gb|CX708839.1|CX708839
EST:     AAATTGTACCGGATGCCCTCNTGAAATTTGGCACACATGTAAAGAAAAAG                         GAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA
genomic: AAATTGTACCGGATGCCCTCCTGAAATTTGGCACACATGTAAAGAAAAAGgtctattttc ... tctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgcaaaacatttgattgattgataaaactataaattttcaatctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCAAAGTCTCAAAAGAAAACATTTGACGACTCTGATGAAGACTAAGTGCTGG
                    gattgat  putative branch site (score: 4)
       aaaacatttgattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctattttcttttccactttatctatgcaccagtttagattttttctatgatggagctaggataaacatttcgttgttttggcaatcctttaactcttgtcttgtgcaaaacatttgattgattgataaaactataaattttcaatctatgatagGAGTCCAAACTTTATGGGGCACACTTCAAGGAAATTCCTGTTGATGCTCCAAAGTCTCAAAAGAAAACATTTGACGACTCTGATGAAGACTAAGTGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA