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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttgttttgatatgcttcttacagggttttgtttaaatttgctacttccatgataggttttgtgtggtaatttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGA

Basic information

species Glycine max
transcript GLYMA02G07250.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 11
ttgtttgttttgatatgcttcttacagggttttgtttaaatttgctacttccatgataggttttgtgtggtaat-ttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGA---
 ||  || |||  | || |  ||   ||    |||| | || || |         |  | ||     |   | | ||   ||| ||||  | |  |   ||||||| |||||||| ||||||||||| ||||| || || |||||||| || ||  ||||| |      | |   | |    |  ||| | || | |  ||   
gtgagtgctttcgtttgttaattttcgg---ctgttcacatatgttta------aacggattccaattcacattgttctcatgtttgtaatccact--cagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAGTACTTCCCTGCGGAGCCGCCAAAG-ATTGCTGAAGC--TGATCACGATAAGCTGGAGTAAATGATGA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 11
ttgtttgttttgatatgcttcttacagggttttgtttaaatttgctacttccatgataggttttgtgtggtaatttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGA---
 ||  || | |    || || ||   ||  |   |      || |    |   ||| |               ||| || |    |     |  |   ||||||| |||||||| ||||||||||| ||||| ||||| |||||||| |||||| |||||       |||  ||| |   ||  ||| | || |  |||    
gtgagtgctgtatcttgtttttttttggcataaatacttcatttcattctgggtgacataacgaactgatgtgtttcctgtctgcgcaacccacttccagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAGATTGCTGAAGCTGGTCA---TGATAAGCTGGAGTAGGAGCGAA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
-ttgtttgttttgatatgcttcttacagggttttgtttaaatttgctacttccatgataggttttgtgtggtaatttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGA
 |      || || |   ||| || | |     || |||    |  |          |      |   |||| |    || | |    | |  ||||| ||||||| ||| |||| || ||||||||||| |||||||| ||||||||  | || |   |||||||||||| ||  ||| |    ||  | || ||| || 
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacact-taaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT

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|51343322|gb|CO984055.1|CO984055
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|298177450|gb|HO023583.1|HO023583
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|10255864|gb|BE823630.1|BE823630
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|21677293|gb|BQ629644.1|BQ629644
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|10254358|gb|BE822124.1|BE822124
EST:     CAAAGCCTTGCAG                         GTNATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCNNNNNTGAA
genomic: CAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|6454129|gb|AW184877.1|AW184877
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|15812369|gb|BI784644.1|BI784644
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|15200443|gb|BI424352.1|BI424352
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
EST: gi|209713090|gb|BW653797.1|BW653797
EST:     TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttccatgataggttttgtgtggtaatttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGA
                                      ttgttcttctttgtt  CT-rich tract
                         taattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttgttttgatatgcttcttacagggttttgtttaaatttgctacttccatgataggttttgtgtggtaatttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGA

-tgtttgt
- - - - - - - -tgcttct
- - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatg