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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG

Basic information

species Vitis vinifera
transcript Vv12s0059g01930.t01
intron # 11
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 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------gttcagtagtctgatttctagt---tcttctgcttctatctccagca------cttctac----tgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG-
                                                                                      |  ||   | || | |||||    |||| |  |   |     || |       || ||     |  ||  |    |  |||| ||       ||    ||      ||||||||||| ||||||||||||||||| ||||| || |||   ||||| |||||||||||  | || ||  || |   |  ||| |||| || |  ||   | | 
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatg-tgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAAT-TATCAGAAAAGA

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGA-TGTGCCACGGATG
        ||| | |||||| |        |||||  |         | ||| ||   ||   |  |  | | || ||||  |            |||||||||| |||||||||||||| || ||||| ||||||  |||||| |||||||||||| | || ||  |  | |     ||||||| | ||||    ||   
--------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggacc--------gcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA-

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgca--tcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG
        || |   |  || |    ||   |||| ||   | | |||| ||| |  |  | || |||| |   | |   | ||     |   | | |||||||||| || ||||||||||| |||||||||||||||  ||   |||| ||||| || || ||||| ||  | |||  |||  | |||  || |||  |  
--------gtttttataatattaacacttaatctaactt-ggtaattctcctgaagttacttgtgtctttttgtt-tgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
gttcagtagtctgatttctagttcttctgc-ttctatctccagcac-ttctactgca---tcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG
              ||| ||     |  ||  | || | ||| ||  ||||  || |    ||||  |  || |   |   | ||| ||   |   | | |||||||||| || ||||||||||| |||||||||||||||  ||   |||||||||| || || ||||||||  | |||  |||  | | |  || |||  |  
-------------gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatgtgctt--ttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG
              ||| || |  | ||        |    |  | |   ||      | || | ||||     | ||     | |||    ||| ||||||||| |||||||||||||| |||||||| ||||||  || ||| | |||||| || ||   |||| |  | | |  |||  |                 
-------------gtttttaatagtcctaaactctaccatggtgcattctcttggctctagtgttttct----ttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------

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|32245481|gb|CD711300.1|CD711300
EST:     GATTGTTCTGCCTTGAATCACTGCTCAGTATGTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGCGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|110418607|gb|EC984768.1|EC984768
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|110385536|gb|EC950069.1|EC950069
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGCGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|110394878|gb|EC960262.1|EC960262
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|110388736|gb|EC953515.1|EC953515
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGCGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|110376126|gb|EC941168.1|EC941168
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTC
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTC
EST: gi|32246966|gb|CD712785.1|CD712785
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|32245954|gb|CD711773.1|CD711773
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGCGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|71870414|gb|DT019469.1|DT019469
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTC
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTC
EST: gi|110423904|gb|EC990257.1|EC990257
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
EST: gi|71870410|gb|DT019465.1|DT019465
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAG
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAG
EST: gi|110422592|gb|EC988919.1|EC988919
EST:     GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG                         CAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT
genomic: GATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagt ... caatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG
                    ttctaac  putative branch site (score: 1)
                                              aatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG