Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG

Basic information

species Glycine max
transcript GLYMA02G17260.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
gtatgataa-tgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
|| ||| |  |  |      | |||||  |       || || |           ||  | |  |||||   |||       ||      ||||||||||| || |||||||||||  ||||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaa-gagatgttggtacaaataaaatg------cagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC

upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
|||||| |||  | | | |  |||   |||||     |  | ||| |   |    |  |   |||      ||||   |   ||     ||||||||||||||||||||||||||| |||| || ||||| ||||| ||||||    | |||||||| ||||||||  ||   | ||| |   |  || |  
gtatgagaatt-ctcctatgattgtgtttcttggattt--tttaagtattattggaaaaaataatt----gacattaatgaagt----gcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC

upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
|||||| |||      || | | | | | |||||   |    |  || || |    ||       |  ||||  | | ||      |  ||||||||||||||||||||||||||| |||| || ||||| ||||| ||||||    | |||||||| ||||||||  ||   | ||| |   |  |  |  
gtatgagaat----tctcctatggatgtgcttctttgtaacatttttaactgtttttgg------gaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC

upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
|||||| |||      || | | | | | |||||   |    |  || || |    ||       |  ||||  | | ||      |  ||||||||||||||||||||||||||| |||| || ||||| ||||| ||||||    | |||||||| ||||||||  ||   | ||| |   |        
gtatgagaat----tctcctatggatgtgcttctttgtaacatttttaactgtttttgg------gaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------

upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttg---tttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
                    ||     || ||    ||| ||| |   | |      |   | |  ||  |  ||   || |    | |    ||||||| || ||||||||||||||||||||||||||||| ||||||||||||||| | |||||||| ||||||||||| || ||||| ||  |  | ||| 
--------------------gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC

upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttg---tttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG------------------------------------------------------------------------------
                    ||     || ||    ||| ||| |   | |      |   | |  ||  |  ||   || |    | |    ||||||| || ||||||||||||||||||||||||||||| ||||||||||||||| | |||||||| ||||||||||| || ||||| ||  |  | |||                                                                               
--------------------gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA

upper sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtatgataatgacacttcttg-------ttgctcttct---tctgcctcgt-gtaatt-gacagcaaatgatgcaatgttaaaacatgccttttgttta----------aacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
           || |  |  | ||  ||  |        | | | | ||   || || | || |||||| |  |    |   | | || |||    |||  | |   ||           ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| | ||||||||||||||||||||||| |||||||||||||||||||
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttgggaatggacacttccat-ttagcttatgtttatgaattggaaattttgcaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG

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|208249782|gb|GE048681.1|GE048681
EST:     GATATTTAAGCCAAGCTCCACTAAATGTTTACGGATACCCGTTACGGCCG                         GGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGT
genomic: GATATTTAAGCCAAGCTCCACTAAATGTTTACGGATACCCGTTACGGCCGgtatgataat ... gtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGT
EST: gi|254331741|gb|GR843591.1|GR843591
EST:     GATATTTAAGCCAAGCTCCACTAAATGTTTACGGATACCCGTTACGGCCG                         GGTGAGAAAGA-TGCTCCTACTATT-GAAA-CGGGGCAGTGCAAATTTGGT
genomic: GATATTTAAGCCAAGCTCCACTAAATGTTTACGGATACCCGTTACGGCCGgtatgataat ... gtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGT
EST: gi|208245673|gb|GE047457.1|GE047457
EST:     GATATTTAAGCCAAGCTCCACTAAATGTTTACGGATACCCGTTACGGCCG                         GGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGT
genomic: GATATTTAAGCCAAGCTCCACTAAATGTTTACGGATACCCGTTACGGCCGgtatgataat ... gtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG
      aattgac  putative branch site (score: 3)
                                       ccttttgttt  putative PPT
                                         ttttgtttaaa  TA-rich tract