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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG

Basic information

species Vitis vinifera
transcript Vv14s0068g01530.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g70100.1 (Oryza sativa), 3'ss of exon 2
atccatgtttatgagttttgtatgtggacctcttagagaaatat-taataaaatataatatgatatcaagtctcagc-tgatagagatgttca--atttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
   |||||  || | || | | |||         ||| || | | |||    |||||     | ||  || || | |    |||  || |     || | |||||  ||    |||||||| || || ||||| || ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||  ||||| | |||||| |
---catgtacataa-ttgtctttgtttggtaaacagaaaagtgtataagtgtatatatgtatacattcagacttaccactttaggaatttctggcatatttcagGACTTGAGCCTTCTACTTCTCACTTCTGGTAGGGATCCAGGTATAATACCTCGGAATGCACACCCTCCAGAACCTGAAGGTTTGGATGGCAATGCAGAGG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G034833_T02 (Zea mays), 3'ss of exon 2
atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgat-atcaagtctcagctgata--gagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
    |     || |  ||      ||| | |  | |  ||     || |||| | |  ||||| |||   ||| |  || |   |   | | | |  | ||||| | |   |||||| || ||||| ||||| |||||||| || || || ||||||||||| || |||||||| |||||||| | |||||  | |||||| |
-cgtacacaaattatcttcagtcatggtcgtgctggtaaagag--aagaaaacagagaatgatcatcccatctaacttgtttacgcattatgccacctttcagGATCTGAGTCTTCTGCTTCTAACTTCTGGGAGAGATCCGGGGATCATACCTCGCAATGCACATCCTCCAGAACCTGAAGGGTTTGATGACAATGCAGAGG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G433942_T01 (Zea mays), 3'ss of exon 2
atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatata-atatgatatcaagtctcagctgat--agagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
    |  |  |  | |||| | ||  | | |  |   |     | || | |||||| | |  | ||    ||| |  || |  ||   | | | |  | ||||| | |   |||||| || ||||| ||||| |||||||| || || || ||||||||||| || |||||||| || ||||| | |||||| | |||||| |
--atacataaaaaaattttatctgaagtcatgatcatgctg-gtaaagagaatatatacaaaacataccctctaacttgtttaagcattatgccacctttcagGATCTGAGTCTTCTGCTTCTAACTTCTGGGAGAGATCCAGGGATCATACCTCGCAATGCACATCCTCCAGAACCCGAAGGGTTTGATGGCAATGCAGAGG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 2
atccatgtttatgagttttgtatgtggacctct-tagagaaatattaataaaatat--aatatgatatcaagtct-cagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
   | | | |     |||   ||     | | |    |  | | | ||   ||| |  | | ||  |     | |  |||||| | |  | |||  |||  |||| |||    || || ||    |||||||| ||||||||||||||||| ||||| ||| | || ||||| || ||||||     |||||| |     ||  
---cttatctgcacatttgtcattaaagcttgtacttactattttcaagggaatctgcactttgtaagtgtatgtatagctga-acatgttttctttttaccagGATTTGACGCTGCTTCTTTGTACCTCTGGTAGAGATCCTGGTATAATACCTCGGAATACTCATCCTCCTGAACCTGAATCCATTGATGGGATCAATGATA

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 2
atccatgtttatga-gttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgtt-caat-ttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
     || || ||   |    ||   | |  ||    |   |   |  ||       | | |||||    ||  | |  ||   |||| | |||| || |||||| |||||||||||  || |||| |||||  ||||||| || |||||||| |||||||| || ||||||||||| |||||||  ||| | | |  ||| |
---ggtgattttgtcatgagatagaagcatatcaccaatttaccatgctatgcacccaaaagatattctttccaaccctatgctgatgctacaatcttttcagGTCTTAGTTCTTCTTTTGTTAACATCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGTTTGGATAGTAATCTAGATG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 2
------atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
      |||  | | | |   |    | ||   |  |  |  |  |  |  ||| || |||| |||  |  | | | |  |||||| |  ||  ||  ||| | |||| |||||||||||  || |||| |||||| |||| ||||| |||||||| |||||||| || |||||||| || ||||||| ||| || |||  ||| |
caacacatcattttctttagatggcat-tgcacatttgctgtactatgagcaatgaagtatattat--ttcctactgtatgctgat-gctataatc--ttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGACGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 1
----atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
    ||       |  ||     | |  |   |   |||      |||  |   || |||   |  |  |||  ||  | ||||    |  |     || |||||| |||||||||||  || |||| |||||  ||||||| || |||||||| |||||||| || ||||||||||| ||||| |  ||| | | |  ||| |
ggtgattttgtcatgagatagaggcaaatcagcagtttaccatgctatgcacccaaaatatattctttccaaccctatgttgatgctaaaatc----ttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGATTAGATAGTAATCTAGATG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 2
----atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
    ||       |  ||     | || |   |   |||      |||  |   || |||   |  |  |||  ||  ||||||    |  |     || |||||| |||||||||||  || |||| |||||  ||||||| || |||||||| |||||||| || ||||||||||| ||||| |  ||| | | |  ||| |
ggtgattttgtcatgagatagaggcatatcaccaatttaccatgctatgcacccaaaatatattctttccaaccctatgctgatgctaaaatc----ttttcagGTCTTAGTTCTTCTTTTGTTAACGTCTGGCCGAGATCCAGGCATAATTCCACGCAATGCACATCCTCCAGAGCCAGAAGGCTTGGATAGTAATCTAGATG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 2
------atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
      ||| || ||| ||  |    | ||   |     |  |  |  |  ||| || |||| |||  |  | | | |  |||||| |  ||  ||  ||| | |||| |||||||||||  || |||| |||||  |||| ||||| |||||||| |||||||| || |||||||| || ||||||| ||| || |||  ||| |
tggcacatcaatttttttggatggcat-tgcacattagctgtactatgagcaatgaagtatattat--ttcctactgtatgctgat-gctataatc--ttttttagGTGTTAGTTCTTCTCTTGTTAACATCTGGCCGAGACCCTGGCATAATTCCACGCAATGCACATCCTCCAGAACCAGAAGGTTTTGAAGGTAGTCTAGATG

upper sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 2
--atccatg---tttatgagttttgtat-gtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
  ||  ||    |||    |  ||| || |  ||     |  | ||   |   ||    ||  | | || |    |  |  || ||      |||   ||  ||||| |||| ||||||| ||||| || || ||||||||||| ||||| || ||  | ||||| || |||||||||||||||     ||||||||     || |
gtatgtatagttttttctcgcattgcatagcagatggtctctataatattctgtagctgatgcttttattttgtattcc--cttatgattccgtttctttcttcagGATTTAATTCTTCTGCTGCTTACATCCGGAAGAGATCCAGGTATTATCCCAAGAAATGCTCATCCTCCAGAGCCTGAAACCCTTGATGGAAACATGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG
                                               tttctc  CT-rich tract
     aatataatatgatatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccatgtttatgagttttgtatgtggacctcttagagaaatattaataaaatataatatgatatcaagtctcagctgatagagatgttcaatttctcagGTTTTAGTTCTTCTACTGCTAACCTCTGGAAGAGATCCTGGTATAATTCCTCGCAATGCCCACCCTCCAGAGCCTGAAGGTTATGATGGAAGTGCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- ccatgtt
- - - - - - - - - -gtatgtg
- - - - - - - - - - - - - - - - - agagaaa
- - - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagctga