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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaccagtgtcaaagccgtagatcccatttagtgtttgatgttattgatatattattcattttttgttgattatgggactcattgcatttcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT

Basic information

species Glycine max
transcript GLYMA09G29070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G29070.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------gttaccagtgtcaaagccgtagatcccatttagtgtttgatgttattg-atatattattcat-tttttgttgattatgggactcattgcatttcaa-----cactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
                                                                          ||||   ||  ||     ||| |    | |  ||||      |  ||   || |||  | | | | || | |||   |   || || ||||||       ||||||| ||||||||||| ||||| ||||||||| | || || || || | |||||| || ||||| ||||||||||| || || |||
gtgaattttaagggctcagatggcatcagtgtttttactttatcttccacgcctttctgtagcttatacttggtttactgatgctaagaat-taggtgtgctatgttgttctgcacttctgcgcattttaaccgtgtctctgatcattcatgtcttcgtt-catttctgtatttcactagGGCTTGGTGCAGCCTGGAAGGTTGCTGATATCTCGAAGGGGTCGAGTGTGGTTATATTTGGCCTTGGAACTGTAGGGCTTTCT

upper sequence: GLYMA09G29070.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G24760.1 (Arabidopsis thaliana), 3'ss of exon 4
gttaccagtgtcaaagccgtagatcccatttagtgtttg-atgttattgatatattattcatttttt---gttgattatgggactcattgcatttcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
                  |||| |   |  || |||||  |   |  ||| ||   |   ||| | |   ||   |  || || || |||  | | ||   ||||||||||||||||||||||||||||||||||   |||||| |||| ||| ||||| ||||||||||||||||| || || |||
------------------gtagttaaaaaataatgtttttaaagtgatgaaatgccaacaattatctatagtcagtactgagaatc-ttgggtgtaaat-ttagGTCTTGGTGCAGCATGGAATGTTGCTGATGTACAAAAAGGTTCAAGTGTTGTGATATTTGGTCTTGGAACTGTCGGTCTTTCT

upper sequence: GLYMA09G29070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0039g00320.t01 (Vitis vinifera), 3'ss of exon 4
-gttaccagtgtcaaagccgtagatcccatttagtgtttgatgttattgatatattattcattttttgttgattatgggactcattgcatttcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
   ||  |   | ||   |||  || |  |||  ||| || | |   | ||   || ||  |||      || |||   ||   | | |||  |    ||||||| || ||||| ||||| |||||  || |  |  ||||||||||||| || |||||||| ||||||||||||||||| |||
gcatattaacttgaacaacgtttattcagttttatgtctggt-tagatcatgagtttttggtttgggtaagaatatttaacaagtggaattatattgttagGTCTAGGAGCAGCTTGGAAGGTTGCCAATATAACCGAAGGATCAACTGTAGTCATTTTTGGACTTGGAACTGTTGGCCTTTCT

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|298197385|gb|HO044864.1|HO044864
EST:     CCTTGCACCTCTTGAGAAAATATGTCTTCTGAGCTGTGAGGTTGCTGCAG                         GTCTTGGTGCAGCATGGAATGTTGCTGATGTG
genomic: CCTTGCACCTCTTGAGAAAATATGTCTTCTGAGCTGTGGGGTTGCTGCAGgtaaacgttt ... tcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTG
EST: gi|209727032|gb|BW680326.1|BW680326
EST:     CCTTGCACCTCTTGAGAAAA-ATGTCTTCTGAGCTGTGGGGTTGCTGCAG                         GTCTTGGTGCAGCATGGAATGTTGCTGAT
genomic: CCTTGCACCTCTTGAGAAAATATGTCTTCTGAGCTGTGGGGTTGCTGCAGgtaaacgttt ... tcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGAT
EST: gi|17519675|gb|BM188717.1|BM188717
EST:     CCTTGCACCTCTTGAGAAAATATGTCTTCTGAGCTGTGGGGTTGCTGCAG                         GTCTTGGTGCATTTATTTAATGTTGCTGATGTGTCAAAAGGATCAACTGTG
genomic: CCTTGCACCTCTTGAGAAAATATGTCTTCTGAGCTGTGGGGTTGCTGCAGgtaaacgttt ... tcaacactagGTCTTGGTGCA-GCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatatattattcattttttgttgattatgggactcattgcatttcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
     atattattcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaccagtgtcaaagccgtagatcccatttagtgtttgatgttattgatatattattcattttttgttgattatgggactcattgcatttcaacactagGTCTTGGTGCAGCATGGAATGTTGCTGATGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT

- - ccagtgt
- - - - - -caaagcc
- - - - - - - - - - - - -ccattta
- - - - - - - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgca