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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcttccaaaattgctaattgtagcctctagtttcatttactcatgcggtcaaaccatccctttatgtttcacttgtggcattggtaacatccaaatctttttttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG

Basic information

species Glycine max
transcript GLYMA03G22790.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
gtctcttccaaaattgctaattgtagcctctagttt-catttactcatgcggtcaaaccatccctttatgtttcacttgtggcattggtaacatccaaatctttttttttc----tcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG
             |||  || ||   | | ||       | |||   |   ||||      || |||  ||     ||     || | |  |||  |||| ||  |||  |     |||| || || |||||||| ||||||||||| |||||||||||| |||||||| | || || || ||||| |||||||| || || |||||||| || |||
------------gttggcaactg--acttttatccagtgtctacctgttaagtca--tttgccattttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 9
gtctcttccaaaattgctaattgtagcctctagttt--catttactcatgcggtcaaaccatccctttatgtttcacttgtggcattggtaacatccaaat--ctttttttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG
               | |  ||   | || |  |      | |||   |   ||||         || |||  |   |      | | || |    ||  |  || |    |   |||| || || |||||||| ||||||||||| |||||||||||| |||||||| | || || |  ||||| |||||||| || || |||||||| || |||
---------------gttggttactggctttcatccagtgtctacctgttaagtcatttgccattttcatgcatt-ttcaaaataattgtcatgagcatgttactgtaccatgtccagCCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 9
gtctcttccaaaattgctaattgtagcctctagtttcatttactcatgcggtcaaaccatccctttatgtttcacttgtggcattggtaacatccaaatctttttttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG
                    ||    | |||   |  ||||   |||| |    |  ||| | ||| | ||    | ||  ||| ||| |        |||||||  |  ||||| ||||| |||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||  | |||||||| || ||||| || ||||||||||| |||
-------------------gtttctccttctccctctatttga-catgtgcctgacacatgcttttgtattaatttagtaacat-ggttatgc-----tctttttgatgttcagCCACACAGAAGACCGTGGATGGGCCTTCAATGAAGGATTGGCGAGGGGGCCGAGGTGCTTCACAAAATATCATCCCAAGCTCCACTGGTGCTGCAAAG

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|151403747|gb|EV273557.1|EV273557
EST:     AGTTGAAGGTTTGATAACAGCGGTACATGCAACAACAG                         CAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAA
genomic: AGTTGAAGGTTTGATGACAACGGTACATGCAACAACAGgtctcttcca ... tttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAA
EST: gi|15589578|gb|BI674194.1|BI674194
EST:     AGAGTTTGGAATAGTTGAAGGTTTGATGACAACGGTACATGCAACAACAG                         CAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAA
genomic: AGAGTTTGGAATAGTTGAAGGTTTGATGACAACGGTACATGCAACAACAGgtctcttcca ... tttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAA
EST: gi|51334832|gb|CO978698.1|CO978698
EST:     AGTTGAAGGTTTGATGACAACGGTACATGCAACAACAG                         CAACACANNAGANNNTAGATGGTNNNTCTATGAAGGATTGGCGAGGAGGAA
genomic: AGTTGAAGGTTTGATGACAACGGTACATGCAACAACAGgtctcttcca ... tttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctttatgtttcacttgtggcattggtaacatccaaatctttttttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG
                         tggtaac  putative branch site (score: 2)
                                       tctttttttttctc  putative PPT
                                    aaatctttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcttccaaaattgctaattgtagcctctagtttcatttactcatgcggtcaaaccatccctttatgtttcacttgtggcattggtaacatccaaatctttttttttctcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC