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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagttcatgagtctaagtgcaataactgttcctaataactaacatatatatgtgtgtgtgtctctgatgtgatataatcatatatacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTCCAGCAATTGACTA

Basic information

species Glycine max
transcript GLYMA12G00830.5
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 7
lower sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
ctagttcatgagtctaagtgcaataactgttcctaataactaacatatatatgtgtgtgtgtctctgatgtgatataatcatat-atacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTCCAGCAATTGACTA
                       ||  ||||  ||||  | || |     | |  | |   ||  ||   |    |  | | |   |   |||||    |||||||| ||  | ||| | || || ||||| || || ||||||||||||||||| |||||||| |||||||||||||| |||||||| ||||  | |   
----------------------gtatgtgttt-taattgcaaata-----acgcttatagttcattgggcttgc-tggttacaccgttgctattttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT

upper sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 7
lower sequence: PP1S62_116V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------ctagttcatgagtctaagtgcaataactgttcctaataactaacatatatatgtgtgtgtgtctctgatgtgatataatcatatatacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTC-CAGCAATTGACTA
             | | |||    || || |   ||||    ||     |||| |   |      ||| |     |||| | ||  |       | |  || ||| || || || || ||  | ||||| |||||  | || || || || ||||| |||||||| |||||||||||||||||||| |||||  |        | ||  || 
tttcgcttggaacattgcatagacctgagagtcttaaccagcccactgtactagc---tgagcaggtgagcagacctgacgcgaggt-------ttttgttgttt-tgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGAGTACGATTACACGATGGACTTTGAACTTGGGGGTCAGTGATAGTTATCT-

upper sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 7
lower sequence: PP1S62_116V6.2 (Physcomitrella patens), 3'ss of exon 10
-----------ctagttcatgagtctaagtgcaataactgttcctaataactaacatatatatgtgtgtgtgtctctgatgtgatataatcatatatacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTCCAGCAATTGACTA
             | | |||    || || |   ||||    ||     |||| |   |      ||| |     |||| | ||  |       | |  || ||| || || || || ||  | ||||| |||||  | || || || || ||||| |||||||| |||||||||||||||||||| |||||  |   |||  |       
tttcgcttggaacattgcatagacctgagagtcttaaccagcccactgtactagc---tgagcaggtgagcagacctgacgcgaggt-------ttttgttgttt-tgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGAGTACGATTACACGATGGACTTTGAACTTGGGGGT--CAGTGA-------

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|31312555|gb|CD397758.1|CD397758
EST:     AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
genomic: AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
EST: gi|192330861|gb|FK021620.1|FK021620
EST:     AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
genomic: AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
EST: gi|31476506|gb|CD418534.1|CD418534
EST:     GGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCCACCATTGA
genomic: GGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
EST: gi|9820599|gb|BE556109.1|BE556109
EST:     AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
genomic: AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
EST: gi|19346154|gb|BM891034.1|BM891034
EST:     AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAA
genomic: AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAA
EST: gi|21887729|gb|BQ740942.1|BQ740942
EST:     AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
genomic: AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
EST: gi|31468734|gb|CD410762.1|CD410762
EST:     AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAA                         GTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA
genomic: AAAATCATTGATGTGTTGATGTCACGCGGAGTTGAGCCTGAAGTTGACAAgtaaaccctt ... atttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatgtgtgtgtgtctctgatgtgatataatcatatatacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTCCAGCAATTGACTA
                 ctctgat  putative branch site (score: 4)
                                          cttatttct  putative PPT
                      atgtgatataatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagttcatgagtctaagtgcaataactgttcctaataactaacatatatatgtgtgtgtgtctctgatgtgatataatcatatatacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTCCAGCAATTGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA