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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttacccactctattgcgataaatttttatgcaacttccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat...

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os05g24550.4 (Oryza sativa), 5'ss of exon 9
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttacccactctattgcgataaatttttatgcaact-tccatggtcaatttctgaaaacccaaaaccatcctat-ttaaaatttataat--
 |  ||||| | |||||||||||| || |||||||| ||||| || ||||| || || ||| | ||||| || || |||||||| || |||||||||||||||       ||| |   | | | | || | ||    ||| |   || | |  || ||   ||     ||| | |||   |   ||   |  | ||  |  |  
TTTCAGTGTCAATGCATACAGAGTAAATTCTGATCCACATGACATAATGGCAGAGGTCTACCAAAATGGCCCTGTAGAAGTTGCTTTCACCGTTTATGAGgtac-cattgacttt---ctattttttttccatgctctttcaccaaattgttgattgttggttagcagaaatcaaaatggactgtaggctgcagttgctgcttt

upper sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
lower sequence: AT4G01610.2 (Arabidopsis thaliana), 5'ss of exon 7
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttaccc----actctattgcgataaatttttatgcaacttccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat
 || ||||||||| ||||||  || || ||| |||| || ||||||||||| || ||||| |||||||| || ||||||||  | |||||||||||||||||||   ||||||   | ||    | | | ||   ||| |  || | | ||  |  ||  | |||   |          |                        
TTACAGTGTTAGTACATACACTGTGAAATCTAATCCACAAGATATCATGGCAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaa--taaaacttaaatcctaagattgtttttgaatagaagttaaagaaagatgtatcattaatggtttgctttggttag-----------------------

upper sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G02300.1 (Arabidopsis thaliana), 5'ss of exon 7
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttacccactctattgcgataaatttttatgcaacttccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat
|||| ||||  | ||||||||| ||||  |||| || || || || ||||| || |||||||||||||| || || || ||||| ||||||||||| |||||||   ||||   ||      |  ||||    |||   |  ||    |  | |||| || | |  |    |    | | |  | ||    |        
CTATGGTGTCGGCGCATACAGAATCAATCCTGACCCTCAAGACATTATGGCTGAGGTTTACAAGAATGGACCTGTCGAGGTTGCTTTTACCGTTTACGAGgtaatgaaaaagattt------ttgattg-atcaaaccatattgattatatcttggtgaagtccacattttcatgtatctttttgttcttcag-------

upper sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 5'ss of exon 7
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttaccc-actctattgcgataaatttttatgcaacttccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat
 ||| ||   |||||||| ||| |||  ||||||||| |  | || ||||| ||||| ||||||||||| || ||||| ||||| || || |||||||||||||| |||| | | |   |  |  |||||  || |||||  ||||| ||     |   |  ||||||      |  |   |   | |  ||    ||  |
TTATGGTCAAAGTGCATATAGAATCAGTTCTGATCCCTACCAAATTATGGCAGAAGTGTACAAGAATGGACCTGTTGAGGTTGCCTTCACTGTTTATGAGgtaaaagaaagcacctgttctgcgttattgttatgaatttg-atgcagctaatgagcatatcttctgacgcatgaccaatttggcactctaagaccatggt

upper sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ05715 (Selaginella moellendorffii), 5'ss of exon 7
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttacccactctattgcgataaatttttatgcaactt-ccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat
||  |  ||     | |||   |||||||| |||    | || |||   || ||  |||||||||||||||| || |||||| | | |||||| ||||||||||| |       |||    | |||  ||       |||| | | ||||  |   || ||||   ||                                 
CTTCACGGTGCAAACTTACGCTGTCAACTCCGATATTTACGACATCCAAGCCGAGATTTACAAGAATGGGCCCGTGGAAGTTTCCTATACCGTATATGAGgtaaaag------tttatgagcgctagagc------ctttttttcgacttatcggtgttaattgtcgatgcag----------------------------

upper sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ32889 (Selaginella moellendorffii), 5'ss of exon 7
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttacccactctattgcgataaatttttatgcaactt-ccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat
||  |  ||     | |||   |||||||| |||    | || |||   || ||  |||||||||||||||| || |||||| | | |||||| ||||||||||| |       |||    | ||      | ||  |||| | | ||||  |   || ||||   ||                                 
CTTCACGGTGCAAACTTACGCTGTCAACTCCGATATTTACGACATCCAAGCCGAGATTTACAAGAATGGGCCCGTGGAAGTTTCCTATACCGTATATGAGgtaaaag------tttatgagcgct------agaacctttttttcgacttatcggtgttaattgtcgatgcag----------------------------

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|13252459|gb|BG363370.1|BG363370
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGCAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|31312156|gb|CD397359.1|CD397359
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|192323979|gb|FK015700.1|FK015700
EST:     CGGAAGTTTACA-GAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACT
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACT
EST: gi|18716048|gb|BM522863.1|BM522863
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|9899704|gb|BE608672.1|BE608672
EST:     TTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: TTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|58018606|gb|CX705348.1|CX705348
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|298182905|gb|HO028118.1|HO028118
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTGCCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAG-TTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|151400974|gb|EV270788.1|EV270788
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|18719713|gb|BM523220.1|BM523220
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|17402160|gb|BM178942.1|BM178942
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|151411964|gb|EV281775.1|EV281775
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCA
EST: gi|8670417|gb|BE191524.1|BE191524
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCANGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|6666111|gb|AW277570.1|AW277570
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
EST: gi|254336334|gb|GR842513.1|GR842513
EST:     CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAG                         GATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA
genomic: CGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaa ... ctcttcacagGATTTTGCTTACTACAAATCAGGAGTTTACAAACACATCACTGGTTATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttacccactctattgcgataaatttttatgcaacttccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccactc