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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctaataactttctatcttaataagtactatattttgtttcttaatgtgaaattgcccttgaagtgatattaatggaactcttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT

Basic information

species Glycine max
transcript GLYMA10G42940.3
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G181151_T04 (Zea mays), 3'ss of exon 5
----gtctctaataactttctatcttaataagtactatattttgtttcttaatgtga---aattgcccttgaagtgatatt------aatg----gaactc--ttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT
    || || | | |  |    || |||    |  |     |||  |    | || |   ||    || | |  |  |  |       |||     |||    | |||      ||  |   ||||| ||  | || ||  | || ||||||||||| ||||||||  | || ||||| || ||||| || || || |||||||||||||||||||||||||| |
gtctgtttcgagtgaaataaattcctaagggcttgttcgggttgcgtgcagacgtaaccgaacaagccctaagttagttctttttcagatgtccaaaacctaatgttctgttacttcttgctcagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATACGACACACGGAACATCTTCCAGTCACTAGATCTTGCATGGACAT

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 13
gtctctaataactttctatcttaataagtactatattttgtttcttaatgtgaaattgcccttgaagtgatattaatggaactcttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT
        |   || | |    ||||| | |  ||  ||  |||||  |  ||     |||   ||      ||||||      || |   || | ||    |||||| ||  | || ||  | || ||||||||||| ||||||||  | || ||||| |||||||| || || || ||||||||||| |||||||||||||| |
-------gtctgttgcgagtgaaataaattc-gtaagttagttctttttcaga-----cccccaaaac----ttaatg------ttctgttccttattgc--acagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATATGACACACGGAACATCTTCCAGTCACTCGATCTTGCATGGACAT

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 14
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
gtctctaataactttctatcttaataagtactatattttgtttcttaatgtgaaattgcccttgaagtgatattaatggaactcttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT
                        |   |  | | || |  ||   |  ||  || |||  |     | ||     |  ||| |||||     ||  |   ||||||| ||||| || || ||||| ||||| ||||| |||||||| || |||||||||||||| ||||| || || ||||||||||| || || ||||||||| 
-----------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctctt-aacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC

upper sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 14
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 14
gtctctaataactttctatcttaataagtactatattttgtttcttaatgtgaaattgcccttgaagtgatattaatggaactcttttccccccttt--tattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT
        ||  | ||  |||||  || ||  || |  |      | |  |||| |  |  ||| |   | |  | |   |   | | |  |||||   |   ||||||| |||||||||||  | || || || |||||||| ||||| || |||||||| |||||||||||||| || |||||||| || ||||| ||||||||  
-------gtacatctcactcttataaattatcatttcat-----ctgaaatgaa-tccctattgtaagaaaacaactaacaggttgtccgacccttcactggaaacagCTATATCTGGAATTCCTAGACAAATTCGAGAGAAAATTTGTGGCTCAGGGAGCCTATGACACCCGCAACATCTTCCAGTCCCTTGATCTGGCATGGACGC

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|13481557|gb|BG510900.1|BG510900
EST:     TGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: TGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
EST: gi|7685689|gb|AW756337.1|AW756337
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
EST: gi|15813509|gb|BI785784.1|BI785784
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
EST: gi|7685559|gb|AW756207.1|AW756207
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
EST: gi|16283344|gb|BI945501.1|BI945501
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     AGGCAATGAAAGCAGTGCTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGCAATTTTTG-AGAAGTTTGAGAGAAAAGTT-GTGGCCCAGG
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGG-AATTTTTGGAGAAGTTTGAGAGAAA-GTTTGTTGCCCAGG
EST: gi|16106409|gb|BI894149.1|BI894149
EST:     GAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: GAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
EST: gi|7686714|gb|AW757362.1|AW757362
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattgcccttgaagtgatattaatggaactcttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT
                   tattaat  putative branch site (score: 2)
                              ctcttttccccccttt  putative PPT
                                           ttttattaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctaataactttctatcttaataagtactatattttgtttcttaatgtgaaattgcccttgaagtgatattaatggaactcttttccccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGAAAGTTTGTTGCCCAGGGAGCTTATGACACCCGCAATATATTCCAGTCACTAGATCTTGCATGGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA