Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttgcatgcatcaaatattaattttgggcatgcaatttaggatttggatcctttgcaattttatgatttacttaattatgcaaagccttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT

Basic information

species Glycine max
transcript GLYMA03G14740.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G14740.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G54130.1 (Arabidopsis thaliana), 3'ss of exon 1
----tttgttgcatgcatcaaatatta-attttgggcatgcaatttaggatttggatcctttgcaattttatgatttacttaattatgcaaagccttttctg-tagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
       | |  ||||      | |   |||||   | |||||  | | || | |   ||||||   ||  |  ||||  | |  ||||      ||   ||  |||| || ||||| ||| ||||||||||||| |||||||| || || ||  | | ||||| ||| |||||||| ||||| ||||||||||| ||||  ||||
aacagagggtttatgcgattggtgtagcattttaatcttgcaaagttg-atctag--tctttgc---ttattcgtttaactgagaatgcttctgtttgattgacagGTCTTGCAAAAAGCTTTGGAAGTGTGGGATCTACAAGTAATTCCACTCAATTGTCCAGATGCAGAGCCTGCGCAGATAGACCCTGAGCTTGAAAGCGCCT

upper sequence: GLYMA03G14740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g01730.t01 (Vitis vinifera), 3'ss of exon 1
tttgttgcatgcatcaaatattaattttgggcatgcaatttaggatttggatcctttgcaattttat--gatttacttaattatgc----aaagccttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
     ||| ||    ||||   ||  |  ||  |    |  | | |    ||    ||      |||       |||| || |||     |||  | | |||| ||||| | ||||| ||| |||| |||||||| || ||||| ||||| ||||| | |||||||||||||||||||||||| |||||||||||||||||||| |
-----tgc-tgggcaaaatgaaaaactgtgggcttttttccatggtgactattgcatggtgccatattcagccaacttgatgatgtgtcaaaattcctgtctgcagGTTCTGCAAAAAGCTTTGGAGGTGTGGGATCTGCAAGTGATCCCCCTTGATTGTCCAGTTGCTGAGCCTGCCCAGATCGACCCTGAGCTGGAAAATGCAT
















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|298171732|gb|HO021324.1|HO021324
EST:     CAGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|12774783|gb|BG239731.1|BG239731
EST:     CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|209729659|gb|BW669759.1|BW669759
EST:     CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|298197044|gb|HO041731.1|HO041731
EST:     CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|17153762|gb|BM143695.1|BM143695
EST:     CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|209724914|gb|BW669603.1|BW669603
EST:     CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAATCGCACAATGTCTCGCTCGACGGCGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggatcctttgcaattttatgatttacttaattatgcaaagccttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
                           acttaat  putative branch site (score: 4)
                                           ccttttctgt  putative PPT
         tttgcaattttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttgcatgcatcaaatattaattttgggcatgcaatttaggatttggatcctttgcaattttatgatttacttaattatgcaaagccttttctgtagGTTTTACAAAAGGCTCTGGAAGTGTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - gcatgca
- - - - - - - - - - - - - - - - - - - - - ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcaa