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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC

Basic information

species Glycine max
transcript GLYMA09G00430.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttctta-aaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttc-----aagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                                                                                     ||    |   || ||  |   |  |||| || | || |           ||| | ||||| | | |||   ||  |||   |   |  |||| |      ||||| || |  ||||||||    ||| | || |  || || | |||  | || || ||||| |||||||| ||||||||||||||||| ||||||||||| |
------------------------------------------------------------------------------------gtaccactttgttctatttcaccaacttacaatgcattct----------acttccctttcacctgcttcctgagcacaacatcccatcatctcttttctgaagGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatcttt-caagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                                                                               ||  ||  ||| |   ||| |  || | | |||    || || | | ||| | |  |  | | |    |  | | ||  || | | | |       ||  ||||||  | || || ||| |    ||||||||  | || || |||||  | || || |||||||||||||| |||||||||||||| || ||||| || ||||
-------------------------------------------------------------------------------gtatcacctagctattttagagtttctttcctttcgagtttcacgttggtagagttt--attgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttct--tcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                                                                                               |||| | ||| ||  ||||  || |     ||  ||         |  |  |  || | ||| ||||  | ||  |         | ||||||| ||||| |||| | ||||||| || || || ||||||||| | ||||| ||||| |||||| | ||||||||||||||||| ||||| |||||||
-------------------------------------------------------------------------------------------gtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataa--tcgtcaa---------ccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                                                                                                  ||    |  || ||    |  |   | ||        |    ||||  |  |  |||        ||  |||  |||   || |||||| ||||| |||| | | ||||| || || || ||||||||| | ||||||||||| |||||||| ||||||||||| || |||||||| |||||||
-------------------------------------------------------------------------------------------------gtaataatgattttttggtgctttattcagtaatattttatcatttcggtaacagttattcctttctgactaatcatcaacca-gGTTGTAGCTATAGCAAGTGCAGCACTTGATGGTTTCAAGAATGAAGCCAAGAAAATGGTGGTTGCACTAGTTGATATGGAACGCGCTTTTGTACCACCTC

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaata-tattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                  || | | |  ||  |||    ||||||  |  |  |   | | |  ||||   | ||      |||    || ||   ||| |   ||  | | ||||   |||  || | |      |  | ||| | ||| | ||        || |||   | | ||   |||||||||| ||||||||| | |||||||| | ||| ||||||||| | ||||||||||| ||||| || || ||||||||||| |||||||| || ||||
------------------gtatattttctttgattgcgcacctgttcttgtgctggcagtatttatttatatattcagg-attgtgcgtaatt---tta-atccttcatacctaaaaa-atctattcgatt----ttttattttatttttttatt------ttttattttttatttttattagGTTGTGGCAATTGCAACTGCTGCACTAGATGTGTTCAAGAATGAAGCTAAGAAAATGGTGGTTGCCCTAGTGGATATGGAGCGAGCTTTTGTGCCCCCTC

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S33_163V6.1 (Physcomitrella patens), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                                                       | | |  |||||  ||   |||  || | || |  |||    ||| || |  | | | |  || |   || ||     | |  | |   |  |||||| ||   |               |||  || |||| || ||||| | ||| || || || |  |  | |  |||||| ||||||||||||||||| || ||||| ||||||||||| ||| |||||||||
------------------------------------------------------gtttgtacaatttcggttccttc--gtagtatctgcttc---gataaatgtggtacattatagtgtg--ttgggctaaaatt--attcaatgattctttgaggctatgcg-----------tttgcagATTGTTGCCATTGCCAGTTCAGCGCTGGACGAATACAGGGTTGAATCAAAGAAAATGGTTGTTGCTCTTGTTGACATGGAGCGTGCATTTATCCCACCTC

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                  ||  || |   | ||| |  | |   ||| || || ||   | || | || | ||         ||| | | |    |||  ||| || ||| |  |   ||  |  |    | |  ||  ||| |  | |    | | || |   || | | |||| | || | |||| || ||||| ||| | || || || | || ||     ||| | ||||||||||||||||| || ||||||||||||||||| ||| | || ||||
------------------gtgcttatagatttatctctttctactatcaa-atgttcactaaattctgtgact---------gcaaaaattatagttacccatctttttcattga---atttcacacaatgtgcttgggcttacagtattcaatggtta-ctcggtgttataatcctgca-gATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC

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|7684962|gb|AW755610.1|AW755610
EST:     CTGCCAATGCTACACCTGGTTTGAGAAGATACCCACCTTTCAAGAGAGAG                         GGTGTGGCTATTGCAACTTCCGCACTAGA
genomic: CTGCCAATGCTACACCTGGTTTGGGAAGATACCCACCTTTCAAGAGAGAGgtattgtact ... atctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
                           agataac  putative branch site (score: 3)
                                              tctttc  putative PPT
                   tttcttttagataaca  TA-rich tract