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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaatcttttccatgtatgcctttgcccttttgtttttttggagcaactctaacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA

Basic information

species Vitis vinifera
transcript Vv07s0031g01970.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 7
-------gtaaagaatcttttccatgtatgcct-ttgcccttttgtttttttggagcaactctaacaatc-----tgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
        |    | |||||    ||| |  || ||| |   |||| ||| |       |||| |  ||      | ||||||| ||||||||||||| || |||||||| ||| | ||||||||||| |||||||| ||||||||||| || || |||||||||||||||||||| ||||| |
gtaggctttccccactctttattttgtttatctgttgtcagattgtgtttctttttt--ctctgaatattttcttttcatgtagATCCTGAGGAAAATATGTTGGTATTTGGTTCTATCACCGCATGATCCAATGCAGTCAAGCCTTCTCAATTCTACCTTGGAGGATAAGAATCTGTCTGAGA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 7
-------gtaaagaatcttttccatgtatgcct-ttgccc--ttttgtttttttggagcaactctaacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
        |    | |||||    | | |  || ||| |   || ||||| |||    |           | | ||||||| ||||||||||||| || |||||||| ||| | || |||||||| |||||||| ||||| ||||| || || |||||||||||||||||||| ||||| |
gtaggctttccctactctttattttatttatctgttgtcagattgtgtttctttttctctgaatattttcttttcatgtagATCCTGAGGAAAATATGTTGGTATTTGGTTCTATCCCCGCATGATCCAATGCAGTCAAGTCTTCTCAATTCTACCTTGGAGGATAAGAATCTGTCTGAGA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 7
------------------------gtaaagaatcttttccat----gtatgcctttgcccttt--tgtttttttggagcaactctaacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
                         |       ||||||  |    ||  |  | ||   | |  | || | ||        | |     | | ||||||| |||| |||||||| || ||||| || ||| |  | ||  |||| ||||||||||||||| |||| || |||||||||| |||||||||||| ||||| |
gtaagccttttttttttcctttttcttttttgccttttctgttattgtgagattctgttatatgatattgtgtttttctgcatattgtcttttacatgtagATCCTAAGGAAAATATGTTGGTACTTGGTTCTAGCGCCCTATGATCCAATGCAATCAAGCTTTCTCAATTCCACCTTGGCGGATAAGAATCTATCTGAGA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 7
gtaaagaatcttttccatgtatgcctttgcccttttgtttttttggagca-------------actctaacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
||||    ||| ||   | | |   | ||   || |||| || ||    |             | | | |   | |   ||||| |||| |||||||| || ||||| || ||| |  | ||  |||| |||||||| ||||||||||| || ||||||||||||||||||||| | ||||| |
gtaagccttctcttttttctgttattgtgagattctgttgttatgcgatattctgtttttctgaatattatcttttatgtgtagATCCTAAGGAAAATATGTTGGTACTTGGTTCTAGCGCCCTATGATCCAATGCAGTCAAGCCTTCTCAATTCCACCTTGGAGGATAAGAATATATCTGAGA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 7
------gtaaagaatcttttccatgtat-----gcctttgcccttttgtttttttggagcaactctaac-aatctgcatg----tagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
        |     |   ||  ||||||     |  |     || | |  ||  || |  |||| |     |||| ||      |||||||||||||| || |||||||  || || ||| |||| ||||||||||||||||||||| | || ||  | ||  |||| || |||||| | || ||||
gtaagctcatgccgttgattggatgtatagttagtatacattctatagggttagtgtaataactttctttgatcttcaaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------------gtaaagaatcttttccatgtatgcctttgcccttttgtttttttggagcaactct--------aacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
                 ||   ||   | ||   ||   | ||  |  || |  ||   |||||  |||| |         |   |||  || ||||||||||| || |||||||||| ||| |  ||| |||| ||||| ||||||||||| ||||| || ||  | |||||||| ||||| ||  | || || |
gtaagtctcgtattgttgtttggatgatctt--gtggtagtctacgttctgtaattagcttggattaacttttctcccttgatcctctaaatatagGTCCTGAGAAAGATTTGCTGGTTTTTGGCCTTGGCACCACATGATCCAATGCAATCGAGCCTACTCAATGCAACCTTGGAAGATAAAAAGTTATCAGAGA

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|351035869|gb|FQ463714.1|FQ463714
EST:     CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATATCG                         GTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
genomic: CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatc ... ctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
EST: gi|110391070|gb|EC956024.1|EC956024
EST:     CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCG                         GTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
genomic: CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatc ... ctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
EST: gi|110381624|gb|EC934958.1|EC934958
EST:     CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCG                         GTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
genomic: CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatc ... ctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
EST: gi|110387763|gb|EC952457.1|EC952457
EST:     GTCAGAGAAGATCCAGCTCAGTGGATACCG                         GTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
genomic: GTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatc ... ctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
EST: gi|110684729|gb|EE062340.1|EE062340
EST:     CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCG                         GTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
genomic: CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatc ... ctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
EST: gi|349825795|gb|FQ423090.1|FQ423090
EST:     CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCG                         GTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG
genomic: CGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatc ... ctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatgcctttgcccttttgtttttttggagcaactctaacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA
                                   ctctaac  putative branch site (score: 2)
                ttttgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagaatcttttccatgtatgcctttgcccttttgtttttttggagcaactctaacaatctgcatgtagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT