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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgctcttatgatttgtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG

Basic information

species Vitis vinifera
transcript Vv08s0040g00430.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 8
gtaagttgctcttatgatttgtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG
  || || |||| || | ||||   ||| |   || ||||| |   |||  |   |      |||| |  |   |  |||  | |   |      |  |  | | ||  ||||| || ||||| |||||||||||||| ||||||||| |||||||||| ||||| || ||||| |||||||| ||||| |||||  |||||
--aatttactct-atcaattgt---ttttactcgtttgtttctcccattctttgatc-----caatttcgtccctctttctgttttcacctccgtatattatgtcttgtagATACAAGAATGACCCTGAAATTTTGGCAATGACAAATTTGATAGCAGCCTATCAGCGTAATGAAATATTGGAATTTGAGAAAATCTTGAAG

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 8
gtaagttgctcttatgatttgtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG
        |  ||||  |  || ||  | |||  |||  || |   |||  |   | |     ||| | ||   |  |||  | |   |  ||  |  |    | || |||||| || ||||| |||||||||||||| ||||||||  |||||||||| ||||| || ||||| |||||||| ||||| |||||  |||||
----tcatcatttattttaagtgtacataatcattgt--ttctcccattctttgatcg-----aatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 8
-----------gtaagttgctct--tatgatttgt---atatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG
           |||  ||| | |  |||  |||     || ||| || | |  | || |||| ||  ||   ||  ||  | | ||  |  | |   || |  ||    | |  | || |  | |||||| || ||||| |||||||||||||  ||||| ||  | ||||| || |||||||| ||||| |||||||| ||||| ||||||||||||
gtaagtcctctgtattttgttttaatatattttactcaatttttcatttctccgattctgttctttatccactga-ggtgaggatcacttctttctgttctcaccttgcatatattctatactgcagATACAAGAATGACCCTGAAATTTTGGTGATGACTAACTTAATAGCGGCTTATCAACGTAATGAAATATTGGAATTTGAGAAAATTCTGAAG

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagttgctcttatgatttgtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG
                                |  ||  |||   |||   | | ||| ||  ||   || || |  ||| |||       | | | |||    | | ||| || ||||| || ||||| |||||||| ||||||||| |||| |||||||||||||| ||||||||  | |||||||| | ||| || |||
-------------------------------gtaagtcatttccgtatatattttttgttg--aacactcgttttggttcgttgc-----ttcatagttggctctctgcagGTACAAAAACGACCCTGAGATTTTGGCAATGACAAATTTGATCGCAGCATATCAACGAAATGAGATCATAGAGTTTGAGAGAATACTAAAG

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|110363999|gb|EC927636.1|EC927636
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACATATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
EST: gi|33405471|gb|CF211098.1|CF211098
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
EST: gi|33405408|gb|CF211035.1|CF211035
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
EST: gi|22015265|gb|BQ800299.1|BQ800299
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
EST: gi|110703379|gb|EE080173.1|EE080173
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
EST: gi|33402297|gb|CF207924.1|CF207924
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
EST: gi|33402377|gb|CF208004.1|CF208004
EST:     ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC                         ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA
genomic: ATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgct ... tcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG
                                cacttac  putative branch site (score: 2)
                                         ttgctcttttcc  putative PPT
              tttgttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgctcttatgatttgtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG