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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtataacaacttcaacacctttatgatgccccttttctactttctttcatacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttcactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC

Basic information

species Glycine max
transcript GLYMA20G36180.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
gtgtataacaacttcaacacctttatgatgccccttttctactttctttcatacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttcactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC
            ||  ||   || ||      | |||||  |     ||| |  |    |  | |   | | | | || | | ||    | || | |   |    | |    | |  ||||  | || |||||||| || |||||||| || |||||||||||||| |||||| ||||| | || || || ||||||||||||||||||||  |||| |
-----------gtttgac---ttcatttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatg-ttataacacaagttaaaacc--actggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC

upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 10
gtgtataacaacttcaacacctttatgatgccccttttctactttctttcatacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttcactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC
                          |   ||  || |||||||  |     | |||   |  | ||      ||| | || | | ||  | ||    | ||  | |  | || |  ||||  | ||||| ||||| || |||||||| ||||||||||||||||| ||||   | ||| | || || ||  ||||||||||||| ||| | ||||| |
--------------------------gtgaccttttctctacttatt-----atggttaatactgcttatgagctatcaagtagt-ctgattattagagaat--gctggcccttttcagGTCTTGCCAACTATTGTCAAGCTTTTTGCCTCCAATGACCGAGCTATCCGAGCATGTCTTTTGCATCACATAAATCAGTTTGGGGAATCAATGTCAGCTC

upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G098078_T04 (Zea mays), 3'ss of exon 10
gtgtataacaacttcaacacctttatgatgccccttttctactttcttt-catacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttca---ctatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC
                                    |   | ||||| | | ||  | | || |  ||   | |  ||  |  |  |  ||| ||  |  ||  | ||  |    || |  ||||  | ||||| ||||| || |||||||| ||||||||||||||||| ||||   | ||| | || || || |||||||||||||| ||| | || || |
-----------------------------------gtgacattttctctacttattgcgattaacactgcttatg-aattatcaagtaatctgata-taatagagaatgccggctcttttcagGTCTTGCCAACTATTGTCAAGCTTTTTGCCTCCAATGACCGAGCTATCCGAGCATGTCTTTTGCACCACATAGATCAGTTTGGGGAATCAATGTCTGCTC

upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgtataacaacttcaacacctttatgatgccccttttctactttctttcatacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttcactatat-agGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC
            ||   || |  |   |     || ||  |      |  | ||        || || | | | ||      | || || || |    ||| |   ||| |  || | |||| || ||||||||||| || |||||||| |||||||| ||||||||  |||||   ||| | |||||| ||||||| ||||| || ||| | || |  |
----------gtttgttcagccatgctaaatttctgtttaaacgctctatacac----tccaatgctgtatgtatacttttcagttattgtc-taaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC

upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gtgtataacaact---tcaacacctttatgatgccccttttctactttctttcatacg-----gtgcttgattc-tctctctctaaccaggatttcttctcatgcttgtattggatttcactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC
                       |||| |   | |   |   ||  ||||     |     || ||  ||  || ||  |      |||||   || | ||| | |  | |  ||||  | |  | |         ||||   |||| |||| ||||| |||||||| |||||||| || || ||||||||||| ||||||||||| || || || ||||||||||||| ||||||||||||||| ||||
gtcatactcttttgagtacctcatgtaaacttattatgttggcatttttaattaacaataattttatctttctttatgtgtttagatgcttatctcatttctgtttttctaaaatttgatgttgt-caaactcctcatttttatatacagGTACTTCCGACAATTGTGAAACTTTTCGCCTCAAATGACCGAGCCATTCGAGTTGGTCTCCTGCAGCATATTGATCAGTATGGGGAGTCATTATCTGCAC

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|37997477|gb|CF809066.1|CF809066
EST:     CATTGCTGAAAATGGGTTCCAGTCTTTCTGCTGAGGAGTTCCGTGTCAAG                         GTGCTTCCAACAATTGTTAAACTTTNTGCATCCAATGACCGAGCT
genomic: CATTGCTGAAAATGGGTTCCAGTCTTTCTGCTGAGGAGTTCCGTGTCAAGgtgtataaca ... cactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctctctaaccaggatttcttctcatgcttgtattggatttcactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC
       ctctaac  putative branch site (score: 2)
                                          tttcact  putative PPT
                                              actatata  TA-rich tract