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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA

Basic information

species Vitis vinifera
transcript Vv14s0060g02240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
           |  ||  || |  | ||||||| ||    |  | |  |   |   |||| |  |    ||  |    |   ||| |  |  |||  ||||||||||| |||||||||||||| || || || || ||||| || ||||| || ||||||||||||||||||||||| |||||||| || || || |||
---------gcaactcacttttcattctcttctcttttatttctaactta--ttattattatgatggtgatggt----gatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
acatatagcataggtctattattttcctcttcttttcctctggtg---agatggctaggtattttagtat-atattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
          ||  || ||| |||   |||   ||| || || |    |  |   ||    | ||| ||| ||||  |    || || || || || ||  ||||||||||| |||||||||||||| || || || || ||||| || ||||| ||||||||||||||||||||||| || |||||||| || || || |||
---------gtaactc-attttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgat-gtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
---acatatagcataggtctattattttcctcttcttttcctctggtgagatggc-taggtatttta-gtatatattttacaa-gtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
   |   | | |    ||   |||||||   | ||||||  | | | |  |     | | |||| || || || |  ||        | ||||    ||||  ||| ||||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||||||||| || |||||||| || || || |||
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
-------acatatagcataggtctattattttcctcttcttttc--------ctctggtgagatggctaggtattttagta-ta-tattttacaagtca-ttgttat-tattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
       | |       | | | |||| ||  |||||| ||||          | | || | |||  |||  ||| |  || || |  || |   || | |||| |  ||||||  ||| | ||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||| ||||| || |||||||| || || || |||
gtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagta-tatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
                                    | ||||    |    ||   | |||         || |  | | ||  |         |  |  || | || |||   | || ||||| || || ||| || | |||||||| || ||||| || || |||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| || || ||||| 
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctg--agtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattt-tgaatc-ttgtt-ttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
                                                                                 |    | |    |  | | | |  || | || | | |  |  ||  ||| | ||  |   |   | ||  | | ||| | | | ||   || | || ||| | || ||||| |||||||| || ||||| || || |||||||| || |||||||||||||||||||| || || |||||||| || ||||| ||||| 
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagatagaatttcacataatgcgaggagttgttgtgcacgactgtaatcattttatatcctgcatgttggatcgttacatggatct-tttaggtctaacatgacctcgtcggtaatctg-cagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA-
                                              |   |  | ||  ||   |   |  |||    |  | |    |   |  || || | |||||||| || ||||| || ||||||||||| ||||| ||||  || ||||  ||||||||||||||||| || ||||| || |||||||| ||  
----------------------------------------------gtgagtgatgttcttcgtttccttctttgtctgaaaat----tcgcttgggtagCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG

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|37189618|gb|CF608967.1|CF608967
EST:     CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATG                         TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
genomic: CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATGgtaagggttg ... attgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
EST: gi|37189144|gb|CF608493.1|CF608493
EST:     CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATG                         TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
genomic: CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATGgtaagggttg ... attgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
EST: gi|110368812|gb|EC932903.1|EC932903
EST:     CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATG                         TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
genomic: CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATGgtaagggttg ... attgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
EST: gi|71886236|gb|DT035291.1|DT035291
EST:     CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATG                         TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
genomic: CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATGgtaagggttg ... attgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
EST: gi|37184974|gb|CF604327.1|CF604327
EST:     CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATG                         TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
genomic: CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATGgtaagggttg ... attgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
EST: gi|37189131|gb|CF608480.1|CF608480
EST:     CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATG                         TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT
genomic: CTTCCTCTTTCTCTGCTCAAGACTGCTCAAGGTCACCCTATGgtaagggttg ... attgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
           tattttagtatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - -ttcctct
- - - - - - - - - - - - -cctcttc
- - - - - - - - - - - - - - - - - - - - - - - gatggct