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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattgtaagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG

Basic information

species Glycine max
transcript GLYMA04G24950.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g54760.1 (Oryza sativa), 3'ss of exon 6
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattg-taagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
 |  || |     ||  ||  |   |   |   |  |||  | || |    | ||||  |  | |  |    |||      | ||      |   ||||||||||| |||||||| ||||||||  |||| ||| |||| || || |||||||| || ||||| ||  || |||| || ||||| |||||||| |||||||
tttttttaaaaaaatgcatttcttgggcaatttacacta-caggtttgccttatacttgaccggtgtgctaattttgtctttacctaccacaatatttcagGTTCCTTTCTTCTCCCAGATGGACAATCAACTTTTGGACGCCATCTGTGAGCGTCTTGTATCATCGTTGTGCACACAGGGCACATACATTGTCCGTGAGG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 6
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattg--taagagtgtttaacaaattccctttctatgctt--tcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
 |  |  ||| | ||| |||   |  |   ||  || |||| ||      |  | || |||    ||    |  | | |||  |  | | |     |   | |||| || || ||||| |||||||||| ||| ||||||||||| || |||||||| || ||||| ||  |||||||    ||||| |||||||| ||||| |
-ttgtc-attgccattaatgt--agcatttcatttgatagtgagatctcgacattctatatcacttactgattctcaccaatctttcataccgcaatgcattagGTCCCTTTTTTCTCCCAGATGGATGGTCAACTTCTGGATGCCATCTGTGAGCGTCTTGTATCTTCCTTGAGCACAGTGGGCACATACATTGTCCGTGAAG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G005791_T01 (Zea mays), 3'ss of exon 5
atgattgattcctattgatgccaatgaacacaaatgc-tagtaagtataaaatttactctatt----gtaagagtgtttaacaaattcc-ctttctat-gc----tttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
         |||| |||   ||  |||| |  | ||| | |||| | | || |  ||  |  |      |  | ||  |   ||||  | |||| ||| ||    || |||||||| || ||||| |||||||||||||||||||| ||||| || |||||||| || ||||| || ||| ||||  ||||||| |||||||| |||||||
--------atcct-ttgccccc--tgaaaaagattgcatcgtaaatttgaactacacattgctttctacataattgcatggtaaatctcgctttgtatcgcaatgttgcagGTTCCTTTTTTCTCCCAGATGGATGATCAGCTTCTTGATGCCATCTGTGAGCGTCTTGTATCATCACTGTGCACAAAAGGCACATACATTGTCCGTGAGG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G436583_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------atgattgattcctattgatgccaatga-acacaaatgctagtaagtataa-aatttactctattgtaag-agtgtt--taacaaattccctttctatgc----tttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
                                                                                   | ||  |||  |   |    || ||   | |   |    |  ||| | |  | | ||   |   | || ||||||  | ||  | ||  ||     ||     | ||||| ||  | ||||| |||||||| ||||||||||| || || ||||| ||||| |||||||||||  |||||||  | ||||| |||||||| || || |
gtaaatcagcttactacctttgctctctcgtttttttattggtcagcaacagagttagtaacttagtagtgctagttgaattcttatccatttgtgaggtgatcagtggcgcgcctctaacggctagtcttacgaataacctgaccatgagtagtgttacttacttaatcttttatatcgcaatgctgcagGTCCCACTTTTCTCCCAGATGGACGATCAGCTTCTAGACGCCATATGCGAGCGCCTGGTATCGTCCTTGAGCACAGAGGGCACATACATTGTCCGAGAAG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattgtaagagtgtttaacaaattccctttctatgcttt-cagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
                        | |       |  |  |  || |   ||       || ||   | | ||     || | |  |  |      | ||||| || || ||||| || |||||||||||||| || ||||| ||||||||||| ||||| || |||||| | ||| |||| || ||| |||| ||||| |
-----------------------gtaagtttttctattgatttgttt---atcctacaaatggttcaacttttaggttaactactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG

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|7924955|gb|AW830981.1|AW830981
EST:     ATCTTCGCCGTGATATACAGCGGCATTTGTGCTTAGACCTTGTTAGAAGA                         GTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAG
genomic: ATCTTCGCCGTGATATACAGCGGCATTTGTGCTTAGACCTTGTTAGAAGAgtatgatttc ... atgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatttactctattgtaagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
                         gtttaac  putative branch site (score: 3)
                                   ttccctttctatgctt  putative PPT
                          tttaacaaatt  TA-rich tract