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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC

Basic information

species Glycine max
transcript GLYMA07G18160.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
                                 |  | || |||  | ||  |  | |   |   ||  |||| ||     ||   |     ||||      | |||| | |  || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| |  |||||||| ||  ||| | |||| ||||| ||
--------------------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatat------tctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC

upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 7
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
                    ||| ||    || | || |  |||     || | || | |  |  |    |   ||||| |||||||   |||| |||| |              ||||||| ||||| |||||||| || ||||| ||||||||||| |||||  |||| ||||||||||| |  |||||||||||| |||  ||||| || || ||
-------------------gtatcttctgatcttccattcttgt----caacttatgc-tgctgagccgaacaaattcaattaatcttc-tgatttatgta-------------ccagGTCTGCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCAC

upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 9
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
                          | | | ||  | |    | |   | |     ||   ||||   |  | ||      |||| |  | || | |  |||||||      | ||||||| ||||| |||||||| || ||||| ||||||||||| || ||  |||| ||||||||||| |  |||||||||||  ||| ||| || ||||| ||
-------------------------gtatcttctgaattctcatcttccagtcttgtcaacttatg--gtgctgatgagaacaatccaattaatct-tctaatttgtgt----accagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC

upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
              | ||   ||  || | |||||  |||||     ||||  | |   || | |||  |  | | | | |  ||   | | |  | || || |        |  |||||||| | ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |||||||| ||  |||  || || ||||||||
-------------gtaagttcatacttttgtcctt--gttatcctgtataa--ggtttcttctttgt--ttctaactgactccatgctggt-acgtgtggaaat--------ctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC

upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatcta-gatgatatatgcaatttgttctt--tcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
                    ||  ||  ||| ||    || | |||  || |  |||| || |   |  | |   |    |   |||  | | ||| |||  |  | |||||  |||  ||||||||||||||| ||||| ||||| || ||||| ||||| || || |||||||| |||||||| || |||||||||||  |||  || || ||||||||
-------------------gtaacttcattttctgatcttgt-tatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC

upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 9
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttctt--tcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
                              | ||  || | | |    |   || ||  |||| |      |||| | || | ||||   |   | ||| |  |||| |||  || ||||||||  | || ||||| ||||||||||| ||||||||||||||||| ||||| |||||||| || || |||||||||||||| ||| |||| ||||||||
--------------------------gtactgctatagatttttgctgtctctgttattttatttcc---tttcact-agatgatcttattctgagatgtatcttgtacttcttcgtcagGTCTCTTGGGTACTGCAGCATTTGCATTCTTCTGCTTCTACCTTCTGCTTGCGGTGATTGCAGGGGCAATGATGCTTGGACTTAGATTAGTTTTCATTAC

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|51335080|gb|CO978946.1|CO978946
EST:     ACTTTCTCCTTTCTTGAATGAAGTTTTCATTAAGCTAGATGATGTCTGGG                         GTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTG
genomic: ACTTTCTCCTTTCTTGAATGAAGTTTTCATTAAGCTAGATGATGTCTGGGgtatgttgga ... ctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaatattcattcagttaatctagatgatatatgcaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
               agttaat  putative branch site (score: 4)
                                       tttgttctttcatc  putative PPT
     atattcatt  TA-rich tract