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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgttttatgttctttttgtggatctggctttcacttgcaatgtagatgttctgcaaattgtggtcacctcattttttttgccttgttttctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTCAAGGGGAAGTCTCTCAC

Basic information

species Vitis vinifera
transcript Vv12s0059g01930.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 7
gtaagctgttttatgttctttttgtggatctggctttcacttgcaatgtagatgttctgcaaattgtggtcacctcattttttttgccttgttttctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTCAAGGGGAAGTCTCTCAC
|||||   |||||  | | || |     |     ||     ||| ||  |  ||||          | ||   || ||   ||||  ||  || | ||||  ||| | || |||  ||| ||  | |||||| || |||||||||||||||| ||||| ||||| ||||||||
gtaag---ttttacatacgttctacatgtactcattcattctgcgata-acttgtt----------tagtgctcttatccctttt--ctcattctttccaaccagGTGCACATTCTCTTTTGTGTTTTTGCTACAATTGCTCCTCCAATTGTCTTCAAAGGGAAATCTCTCAC

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G37590.1 (Glycine max), 3'ss of exon 7
gtaagctgttttatgttctttttgtggatctggctttcacttgcaatgtagatgttctgcaaattgtggtcacctcattttttttgccttgttttctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTCAAGGGGAAGTCTCTCAC--------------------------------------------------
              ||   ||||    |  |    |  |||||   |  |    |||| ||       ||   || ||  ||||| ||   || | |||| |||| | || |||  ||| ||| | | |||| ||||||||||||||||| | ||||| ||||| ||||||||                                                  
--------------gtaagttttacatactt----tctacttgtgct-cattcattctaca---ctaagttctcttatcctttttccc--attctttccaagcaggtgcacattctcttttgcgtttatgctgcagTTGCTCCTCCAATTATCTTCAAAGGGAAATCTCTCACGTGAGTCCCTTTTTAAAACTGCATTCCTTTTATTTAATCTGCTACCTGGC
















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|110418607|gb|EC984768.1|EC984768
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|77584192|gb|DV221151.1|DV221151
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|27586086|gb|CB008781.1|CB008781
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAG
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAG
EST: gi|110385536|gb|EC950069.1|EC950069
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|110388736|gb|EC953515.1|EC953515
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|110376126|gb|EC941168.1|EC941168
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|110357026|gb|EC920280.1|EC920280
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|32245954|gb|CD711773.1|CD711773
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|71870414|gb|DT019469.1|DT019469
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|110699817|gb|EE077160.1|EE077160
EST:     GACTGATAGTGCTCTAAAAGT-CGGGGGGTTTTTCTTGTTTTACCTG                         CTTCATAT-GCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAAT
genomic: GACTGATAGTGCTCTAAA-GTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAAT
EST: gi|71870410|gb|DT019465.1|DT019465
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTG                         CTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTC
EST: gi|110722937|gb|EE099679.1|EE099679
EST:     GACTGATAGTGCTCTAAAGTTCGGGTGGGTTTTCTTGTTTTAACGG                         CTTCATATTGCCT
genomic: GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgtt ... ctccatgcagCTTCATATTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgttctgcaaattgtggtcacctcattttttttgccttgttttctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTCAAGGGGAAGTCTCTCAC
                   tcacctcatttttttt  CT-rich tract
                        tcatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgttttatgttctttttgtggatctggctttcacttgcaatgtagatgttctgcaaattgtggtcacctcattttttttgccttgttttctccatgcagCTTCATATTGCCTTCTGCATCTTTGCTTCAGTTGCTCCTCCAATTGTATTCAAGGGGAAGTCTCTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC