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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattctggataatggatttggaaacatcaatttctctttaatctcattcttgtcatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAA

Basic information

species Glycine max
transcript GLYMA09G01820.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 9
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------gtgagcattctggataatggatttggaaacatcaatttctctttaatct-cattcttgtcatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAA
           |  | || | ||| |  |     ||     |     ||| |||   ||  |||  | ||  |  ||    | ||||||| |||||||| ||||||||||| ||||| |||||  | || || || || || |   | |  ||| ||||||  ||  |  || | 
gtttcactcgtgctaacact-tggtttctcaggctgatgtgaatgtattcacttggttcagcatattggttttttataatgc-agATAGGAACAGATATAGAAGATTTCAAATGCTCGTGGTTGGTGGTTAAGGCATTAGAGCGCTGCAGCGAAGAACAAACTAAGATATTATAT

upper sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------gtgagcattctggataatggatttggaaaca--tcaatttctcttta---atctcattcttgtcatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAA
                                        || |   |  |  || ||  || |  || ||  |  |        ||   |||| | | ||  | | ||||  ||||||| || || |||||||||||||| ||||||||||||||  ||||||||||  | ||  || |||||||  |||| || |||    || | 
gtaagtttcagggttactacactcatttggtttgtggaatgtaattgtatta-atcatcaatatataaccagtttgagcaaagaatatggatcttagtgttacctttcatgctaccagATCGGAACGGATATTGAAGATTTTAAGTGCTCTTGGTTGGTTGTGAAAGCACTAGAGATTTGTAATGAGGAACAGAAAAAAACCTTATAT
















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|192325137|gb|FK017523.1|FK017523
EST:     GATGATTTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAG                         ATAG-TACAGATAT-GA-GATTTCAAGTGCTCT
genomic: GATGATT-ATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCT
EST: gi|19269348|gb|BM885604.1|BM885604
EST:     GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGG--A-                         A-AGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC
genomic: GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC
EST: gi|193491608|gb|FK454242.1|FK454242
EST:     GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAG                         ATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC
genomic: GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC
EST: gi|7028813|gb|AW458596.1|AW458596
EST:     GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAGAG                         ATAGGTACAGATATTGAAGATNTCAAGTGCTCTTGGTTAATTGTGAAAGCC
genomic: GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC
EST: gi|7284732|gb|AW597282.1|AW597282
EST:     GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAG                         ATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC
genomic: GATGATTATTTGGATTGCTTTGGTGATCCTCAAACAATTGGAAAGgtgagcattc ... atgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttggaaacatcaatttctctttaatctcattcttgtcatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAA
                      ctttaat  putative branch site (score: 4)
               aatttctctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcattctggataatggatttggaaacatcaatttctctttaatctcattcttgtcatccatgggaccagATAGGTACAGATATTGAAGATTTCAAGTGCTCTTGGTTAATTGTGAAAGCCTTGGAACTTAGTAATGAACAACAAAAGAAAGTTCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA