Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatttcttgaatttctgtgcttaatgttttgctttttggggggtttctctatgttgattaaagtttaaatagttgtattttggtctatctctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCACAGGAGCGTAAGT

Basic information

species Glycine max
transcript GLYMA13G36410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G36410.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G179429_T03 (Zea mays), 3'ss of exon 2
gtatttcttgaatttctgtgct-taatgttttgctttttggggggtttctctatgttgattaaagt-ttaaatagttgtattttgg--tctatctctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCACAGGAGCGTAAGT
    | |    || ||||   | ||||   ||| |  ||  |   |   |       ||  ||||  | | | |||   ||    |   || | |  ||| ||||| || |||  |||||| || ||| ||      |||||||| || ||    |||||| |||||  |||||||||||||||||||||||| ||| |  | |
----tacaattatgtctgccatataattccttggtggttttgatttccattcggaaagaaaaaagaatcagaaagtgacatgaaagaaactcttttcttgcaagGCCGAAGAACCTGCACGGGATTCATGGAGGAGTAAACAAGACCGATACGACGAAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAAT

upper sequence: GLYMA13G36410.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G27120.2 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------------------gt-atttcttgaatttctgtgcttaatgttttgctttttggggggtttc---tctatgttgattaaagtttaaatagttgtattttggtctatctctttggaa--gGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCACAGGAGCGTAAGT
                                                                                     || ||   || |  ||| |  ||||| | |      || |  |  | |    ||| | |||   |    ||   |  ||   || || ||| | | ||||| |  ||||||||||| | |||| |||||||||  | ||||||||||| | ||| ||||||||||||||  ||||||||| || || |||||| | ||||  ||||
gtgagatttttctatttattctactagaatttttggcaggattaaggatgagaaattctaggaatatcagttggtaagttacattgtgatagttttagattccg-acttaaggatagagcattggcagaatattacatctcttttggg-acgactttcctgattaagttctgttctttttttttggtatagGCTGAGGAAGCTACACGCGAGTCAAGGAATACAAAACAAGATTGGTATGCAGAAATGCGGAGGAAGAAGGATGAAGAACGCGAGGCAGAAGAGCTGAAGT

upper sequence: GLYMA13G36410.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0177g00150.t01 (Vitis vinifera), 3'ss of exon 3
-gtatttcttga--atttctgtgcttaatgttttgctttttggggggtttctctatgttgattaaagtttaaatagttgtattttggtctatctctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCACAGGAGCGTAAGT
 || || ||  |  ||   |||| ||  |||| |  || ||       || |  |  || | |||  |||  |    |   || || | | |    ||| ||||| || |||| |||||| |||||||||||  ||||||||||  | ||| |||||| | |||||  ||||||||||||||| || ||| |||||||  || 
agttttcctacatgatccttgtgatttttgttcttattcttttccttgttttgaagctttagtaa--tttgcaactctaagttctgatttgtaatcttg-aagGCCGACGAAGCTGCACGTGAGTCAAGGCTAACAAAACAAGACAGATATGCAGAAACGAGGAGGAGGAAGGATGAGGAGCGCGAAGCAAAGGAGCGCCAGC

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|193380062|gb|FK347824.1|FK347824
EST:     CATCAAAG-AAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGAGTCAAGG
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGG
EST: gi|254333679|gb|GR848597.1|GR848597
EST:     CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
EST: gi|298170691|gb|HO019315.1|HO019315
EST:     CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
EST: gi|193336863|gb|FK305343.1|FK305343
EST:     CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGAGTCAAGG
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGG
EST: gi|23727933|gb|BU762006.1|BU762006
EST:     CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
EST: gi|51335568|gb|CO979434.1|CO979434
EST:     CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA
EST: gi|193424351|gb|FK386854.1|FK386854
EST:     CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAG                         GCTGAGGAAGTTGCACGAGGGTCAAGGCTTGCAAAACAAGATCGTTATTCA
genomic: CATCAAAGAAAAAGGAGATTAAAAGGCAAGAGAGGGAAGAAAGGCGTCAGgtattctctc ... tctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctatgttgattaaagtttaaatagttgtattttggtctatctctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCACAGGAGCGTAAGT
       tgttgat  putative branch site (score: 4)
                                       tctatctcttt  putative PPT
         ttgattaaagtttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttgaatttctgtgcttaatgttttgctttttggggggtttctctatgttgattaaagtttaaatagttgtattttggtctatctctttggaagGCTGAGGAAGTTGCACGAGAGTCAAGGCTTGCAAAACAAGATCGTTATTCAGAAATGCGGAGGTTGAAGGATGAGGAGCGTGAGGCACAGGAGCGTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - tctgtgc
- - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - -tgggggg