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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcgatacccttgagtcattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA

Basic information

species Glycine max
transcript GLYMA01G02840.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G10490.2 (Arabidopsis thaliana), 3'ss of exon 10
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaa-taatcgatacccttgagtca------ttcttttgagcattgat-gttttcatgc-tgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
           |  |   | | |  || ||   || |||||| || |  ||  |  |    |  |  ||    ||  | | || | || |  | | |      |   |||  | |||| | |||   |||| | | ||||||||||| ||||||||||||||||| || ||||||||||| || || ||  ||||||| |||||||| || || ||||| ||||| ||| | |||||||
---------gttagaatctctgagcttagatgatgtgaattttttcc--tagcttcggtgcacgtcattgccatacctgaacgtttccttaaaattagctagctatctttctgaattgcttgttgcaatgcatttacagCATGTTGGTTGGTGGTCACCAACAATCATAAGAGGTGAAGACCGCGAGGCAATTCACATCCCAAACCATAAGTTCACAGTTAATGTCGTGAGAAACCTTA

upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0313g00020.t01 (Vitis vinifera), 3'ss of exon 10
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcgatacccttgagtcattcttttgagcattgatgttttcatgctg--tgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                      | ||  |||   ||     ||||    | |||  | | |  ||    ||   | | |  ||| |  ||   | ||| | | ||   |||||  | |  || ||  | |||||||| || |||||||||||||||||  | |||||||||||||||||||| || ||||||||||||||||| || || |||||||||||| | || || |
----------------------agttaagaaatcggttgcctctt----tgaattggaaaatgatgagatgccaagtca--gatgcattt---ttattgtct-gaattttgataatcttttgttgcctacagCATGTGGGATGGTGGTCACCAACAATAGTAAGAGGTGAAGATCGTGAAGCAGTCCACATTCCAAACCACAAGTTCACTGTGAATGTTGTGAGAAATCTCA

upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcg-atacccttgagt-cattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                              | ||  |    ||  |  ||   | | |    || |  |     | |||  |  ||   |  | | |  |||  ||||  | | ||||   ||  ||  ||| ||||||| |||||||| || ||  | |||||||| || |||||||||||||||||||||||||||||||| || |  || | ||| || || ||  | |
----------------------------agacgtaaggtgctccgaagtt---tctctgtgttagtgatctgacactaacagtgtattttgtactgcgatctactgagactcggtgttgaaat-ttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA

upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S28_223V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacatta-aatatgtacaatattttttgtgtaataatcgatacccttgagtcattcttttga--gcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                                   | ||||    |||    ||||||||   ||| |||     | | |  | |||    |  || ||  ||||   | | | ||  ||  |   |||  |||||||||| |||||||| |||||  | ||| |||| || |||||||||||||| || |||||||| |||||||| |  ||||  || || || ||  | |
--------------------------------agagtaattcaaaacaccgcaatatgtatg-tatatttctgacattgactggtacatacggctccttgatttgcttggacttattattataacatgtatagCATGTTGGGTGGTGGTCTCCAACTGTGATTCGAGGAGATGATCGTGAAGCTGTCCATATTCCAAATCACAAATTCAGTGTGAGCGTAGTCCGCAATTTGA

upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S58_129V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcgatacccttgagtcattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                      | |     || |  | |  | |   | || ||       ||  |        |||| | || |   ||   ||  | |  | |  ||||||  ||| |  ||   |||||||| || |||||||| |||||  | ||| |||| || |||||||||||||||||||||||||| ||||| ||||  ||||  || || || ||| | |
----------------------attccatgatattcgcaagtttcgaactatat-----tgatgatcagacaccaatagt-gaaatatttatttcgatttacttaaaattgat--tttaaatctacacagCATGTCGGATGGTGGTCTCCAACTGTGATTCGAGGAGATGATCGTGAAGCTGTTCACATTCCAAATCACAAGTTTAGTGTGAGCGTAGTTCGTAACTTGA

upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ18544 (Selaginella moellendorffii), 3'ss of exon 6
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcgatacccttgagtcattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                                                 |  ||| ||| | | | | || |  |  ||  | ||  ||   | | |||           ||||||||||         |||||||||||||||||| || ||| |||| ||||| |||||||| |||||||| || || || |||||||| || ||  |||  ||||| || ||  | |
--------------------------------------------gttggttgatacgtaaattgtgtgttat--agcaaatggtaatctaatgcctttc-----------gatgttttca---------gCATGTTGGCTGGTGGTCTCCTACAGTTATCAGAGGCGAAGATCGCGAAGCTGTGCATATACCCAACCACAAGTTCACGATGAGCGTTGTCCGCAATTTAA

upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ36514 (Selaginella moellendorffii), 3'ss of exon 6
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcgatacccttgagtcattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                                                 |  ||| ||| |   | | || |  |  ||  | ||  ||   | | |||           ||||||||||         |||||||||||||||||| || ||| |||| ||||| |||||||| |||||||| || || || |||||||| || ||  |||  ||||| || ||  | |
--------------------------------------------gttggttgatacgtaaatcgtgtgttat--agcaaatggtaatctaatgcctttc-----------gatgttttca---------gCATGTTGGCTGGTGGTCTCCTACAGTTATCAGAGGCGAAGATCGCGAAGCTGTGCATATACCCAACCACAAGTTCACGATGAGCGTTGTCCGCAATTTAA

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|193549712|gb|FK509661.1|FK509661
EST:     AATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTGGTACAGTCGAG                         CATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCT
genomic: AATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTGGTACAGTCGAGgtgtgttgta ... tgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatcgatacccttgagtcattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
                               cattgat  putative branch site (score: 4)
                                       ttttcat  CT-rich tract
                    attctttt  TA-rich tract