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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgcttttcaatttattattattattattattattcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa...

Basic information

species Vitis vinifera
transcript Vv04s0008g01750.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 2
AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgcttttcaatttattattattattattattattcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa
 | || || || |||||||| ||||| |||||||| ||  | || || || |||||||| ||||| ||||| |||||||| ||||||||||| ||||||||||  |  |||| |  |       |    || |    | |  |   |    ||| |   | | || | |||| |   || | |||  |            
CGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgcttctacaagccccgtcccgatcacagctgtgaatacttcggttactga-actgtttttttctctcgatc-tcgcttag------------

upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EDP07493 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgcttttcaatttattattattattattattattcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa---
 | || || || |||||||| ||||| || || || ||  | || || || |||||||| ||||||||||| || || |||||||||||||| || || ||| |          ||               |     | ||        |       |   | | | ||   | | |    |    | |   | |||  |   
CGCGAGCTGGCCGAGGATGGCTACTCCGGTGTGGAGGTCCGCGTGACCCCCATGCGCACTGAGATTATCATCCGCGCTACTCGCACTCAGAACGTGCTGGgtgagcgcagagagcaggcctcggagggagatggggctcttgg--cagccgccgcggtgcctgt-acatcactcgctgagctatgtgcagcgctttgtgactg

upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgcttttc--------------------aatttattattattattattatta---ttcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa---------------------------------------
 | || |||||||| ||||| ||||| ||||| |||||  | || ||||| ||||| || ||||| ||||| |||||||||||||| ||||| ||  | ||||  ||     |||                     |||||   || || |     |     || | |        | | |  || || | || ||| |||  ||  |   |  |   |  ||                                       
CGGGAGCTTGCTGAAGATGGGTACTCTGGCGTGGAAGTGCGCGTCACTCCCATGCGTACCGAGATCATCATCCGTGCCACTCGCACCCAGAACGTGTTGGgtacgttgatcgttctggcggcttagagtgggagagatttagggtttttgtgcgggtggagtttgagtaggaagcgaatgtgtttttttttttttttttttttttttttaaattattctttaacttggtcttgaggattgactgttcgatcttgtgatgcag

upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 2
AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc---ttttcaatttattattattattattattattcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa
 | || || || |||||||||||||||||||| || ||  | || || ||||||||||| ||||||||||| || || || || || ||||  ||| | ||||| ||  |   |||  |      |    ||| ||  |   || | | ||                                                    
CGGGAGCTAGCGGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGATGCGCACCGAGATTATCATCCGGGCGACGCGAACGCAGAGCGTTTTGGgtaaattcccctgtttctaggcggattcacttagtaaaagctttgattctag---------------------------------------------------

upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ31296 (Selaginella moellendorffii), 5'ss of exon 2
AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgcttttcaatttattattattattattattattcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa
 | ||  | || |||||||||||||||||||| || ||  | || || ||||||||||| ||||||||||| || || || || || ||||  ||| | |||||  |    | |   |       |    | | ||   ||  |||                                                      
CGGGAGTTAGCGGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGATGCGCACCGAGATTATCATCCGGGCGACGCGAACGCAGAGCGTTTTGGgtaaactcctctgtttctaggcggattcactcagtaagctttgattctag--------------------------------------------------

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|71866153|gb|DT015208.1|DT015208
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|30295730|gb|CB972524.1|CB972524
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|32247633|gb|CD713452.1|CD713452
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|32270022|gb|CD719181.1|CD719181
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|33401617|gb|CF207244.1|CF207244
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|110728527|gb|EE104173.1|EE104173
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|352773252|gb|FQ470839.1|FQ470839
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTTGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|110690223|gb|EE067133.1|EE067133
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|110732469|gb|EE107785.1|EE107785
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|32269891|gb|CD719050.1|CD719050
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|110688348|gb|EE066796.1|EE066796
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|77578758|gb|DV218182.1|DV218182
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|27582088|gb|CB004783.1|CB004783
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|110709636|gb|EE085271.1|EE085271
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|32272105|gb|CD721264.1|CD721264
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|30253062|gb|CB970613.1|CB970613
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|352782408|gb|FQ470311.1|FQ470311
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|30326710|gb|CD009972.1|CD009972
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|161706215|gb|FC054973.1|FC054973
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
EST: gi|110708853|gb|EE086870.1|EE086870
EST:     GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCG                         GTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT
genomic: GATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgc ... tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGATGCGCACGGAGATTATCATTCGTGCCACTCGCACTCAGAATGTTCTCGgtaattttgcttttcaatttattattattattattattattcaatttatcattattattattattatattctttgtttcattgctgggaaaacgttggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaaaa