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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC

Basic information

species Vitis vinifera
transcript Vv10s0003g01640.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 12
gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC
        ||  ||||  || | |||   ||| |  ||    ||||      | |  ||| ||     |   |      |  |||     |  ||     ||  ||   |          || ||||| |||||||| ||||| || ||||| ||||| ||  |||||||||| ||||| || ||  | |||||||| ||||||||||||||| ||||||| ||  |||||
-------gtttgttct--ttgtactagttttactatatg---acatcatcagaataaatgagcactgtaatcgtccgattgtttggaa-gtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 12
gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC
                                            ||  |  ||  || ||||||      |     ||  | |    | || | ||   |   || |  |      |||   ||| | ||||||||||||||||||||| || ||||| ||  |||| || ||||| ||||| || || ||||||||||||||||| ||||| || ||||||||| |||  
------------------------------------------gtatagccttatctt-tgtgcttctttcccctccattgtttaccctgatatacttaatcttttgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G12480.1 (Glycine max), 3'ss of exon 12
gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC
                                    |||  |  || | ||| |||    | |           ||| | || |      |  |||  | |  |   | |||    |||   ||| | ||||||||| ||||||||||| || ||||| ||  |||| || ||||| ||| | || || |||||||||||||| || ||||| || ||||||||| |||  
----------------------------------gtatagccttatctttgtggttgtctttcccctccattttttaccctcatatactttaatcttttgttgtacaccttt----ttgtgtcacatttagGTTTGTGCATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGAATCGATCTAAGTAAACAGCCTCCCGCCGTTCGATTAAACAAGGAACTGGAT

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|351013609|gb|FQ429750.1|FQ429750
EST:     CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAG                         GTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
genomic: CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAGgtttaatatt ... ccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
EST: gi|161721461|gb|FC070452.1|FC070452
EST:     CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAG                         GTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
genomic: CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAGgtttaatatt ... ccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
EST: gi|351019257|gb|FQ429417.1|FQ429417
EST:     CTTCCAGTATCAAGCATAGGGGCATATATAAAGGATCCCATCACTCCCAG                         GTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
genomic: CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAGgtttaatatt ... ccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
EST: gi|110361661|gb|EC925153.1|EC925153
EST:     CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAG                         GTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT
genomic: CTTCCAGTATCAAGCATAAGGGCATATATAAAGGATCCCATCACTCCCAGgtttaatatt ... ccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC
                                           ctccactt  CT-rich tract
                           ttatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA