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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttgctgatatgcatttggcagaataattgtcttctttctttcatgcaatgacaagtttcatttgaaattcttaatttttcttctcatatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCAGGATCAAAGCTGCTCTTTGGGGGTAGTCCTCTAGAGAACCATTCAATTC

Basic information

species Glycine max
transcript GLYMA05G01300.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G01300.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 12
-tcatttgctgatatgcatttggcagaataattgtcttctttctttcatgcaatgacaagtttcatttgaaattcttaatttttcttctcatatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCAGGATCAAAGCTGCTCTTTGGGGGTAGTCCTCTAGAGAACCATTCAATTC
   |||||    | |   | ||||| | | |  | |    | | ||  || |||   |    |  ||| ||  | ||||||| | || || | | ||||||| ||| ||||     ||||||||||| | |||||| |||||| |||||||||||||| |||| || ||||| || |   || |||| || ||||| || |
tctatttggatctgtttgtatggcaaagtcacagccaatatcccttt-tgaaatcctattgatatttttaatatgttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC
















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|16995634|gb|BM085006.1|BM085006
EST:     TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACA                         TGTACGACTGGTATGATGCTAAAACAC
genomic: TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACAgtaagtgttt ... tatgttgcagTGTACGACTGGTATGATGCTAGAACAC
EST: gi|9898827|gb|BE607795.1|BE607795
EST:     TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACA                         TGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
genomic: TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACAgtaagtgttt ... tatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
EST: gi|8826963|gb|BE210693.1|BE210693
EST:     TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACA                         TGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
genomic: TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACAgtaagtgttt ... tatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
EST: gi|193551899|gb|FK507298.1|FK507298
EST:     TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACA                         TGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
genomic: TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACAgtaagtgttt ... tatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
EST: gi|8827894|gb|BE211624.1|BE211624
EST:     TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACA                         TGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA
genomic: TTGCTGAGAGAAGAAAGCTAGAAGACTTGACAATCGGCCCAGTCCTCACAgtaagtgttt ... tatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcaatgacaagtttcatttgaaattcttaatttttcttctcatatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCAGGATCAAAGCTGCTCTTTGGGGGTAGTCCTCTAGAGAACCATTCAATTC
                           tcttaat  putative branch site (score: 3)
                                 tttttcttctcatat  CT-rich tract
           aagtttcatttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttgctgatatgcatttggcagaataattgtcttctttctttcatgcaatgacaagtttcatttgaaattcttaatttttcttctcatatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCAGGATCAAAGCTGCTCTTTGGGGGTAGTCCTCTAGAGAACCATTCAATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - -tgctgat
- - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - tgacaag