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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT

Basic information

species Vitis vinifera
transcript Vv14s0060g02260.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 9
agagttctgtgatgtttttatgtactatcacgtattgaaacttttg--agctcta-ccatgggagcaagtactaatcggactgt---caaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT
       ||| |   |  |  | | | | |  ||    |  | ||   | |||||   |||     || ||||  | |     |   |  || | ||      |||||||  |||||||||||||||||||| ||||| || || ||||| |||||||| || ||| |||||||||| || ||     ||   | | |    ||| 
------gtgttaatctgcttggcattgttagataagctatttgttaccaactctaattatgttgataactacttgtggtttcttatcctgatcgtttcttgcgcagGTGACTCATGAGGACTTCAACGAAGGCATAATACAGGTGCAGGCTAAGAAGAAGTCTAGCCTAAATTATTACGCTTAACAAGCTATGCTAGAATCATCAG

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 9
-agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcgga-ctgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT
 || ||    ||       |    || | |   || |     || ||   | ||||    |    | |  |  |   | ||||    ||| |   |    ||||||||||||||||||| || |||||||| |||||||| || || ||||||||| ||||| | ||||||||||||||||||     |   |||| |  ||
cagtgtcaattgtcaaagctccacaccaacttataatttgttttgtgtattttacctgatgttggaatgttcgtaaaatctgttt--ttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
-agagttctgtg--atgtttttatgtactatcacgtattgaaactt--ttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGC-TTCTCCTCCAAACATGTCAT
   | |||  ||  |    |||      | | |    ||| ||| |   |  |       ||| ||  || || |||  | |   |    || ||   ||| |||||||||||||||||||| || ||||| || || ||||| || || ||||||||| ||||||| |||||||||||||||||  ||  | | |   |   |  
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaa--gaatgatt---tttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG-

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 6
agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT
  | |||  ||       | || || ||     | |      | |||      |       |  |  | | ||            || ||   ||| ||||||||||||||||||||  | ||||| || || ||||| || || ||||||||| |||||||  ||||||||||||||                      
gcaattcaatgccaaagctttggaccatgttagaatttgtaatatgaatgtgtctgcttacgtgaaaaatcattaagtatgattttttgtccaattgcagGTGAACCATGAGGACTTTGATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGGATTATTATGCATAG----------------------

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 9
-agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT
     ||| || |      |    || | |  ||| |     || |    | ||||    |    | |  |  | | | | |    ||| |   |    |||||||||| ||||| || || |||||||| |||||||| || || ||||||||| ||||  | || |||||||||||||||         |||| |  ||
ttcttttcagtaacaaaactccagaccaacttgtaatttgttttatatattttacctgatgttggaatgttcgt-gaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT-
             || |  || ||   |  ||| ||     || | | || ||  ||| |    | ||   |  | | ||  ||||  || ||    ||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||| ||||||| ||||| || || || | | ||| |  |   |     | 
-------------gtatgcatatatcttt-cgtcttagtggttgtaa-ctttaggatgtggatga-tatggag-gaaatggtaaatgtgtgtg----cagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAG-TCCTCTTTTATGTACACTCTT

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT
           |||  ||| | ||| ||| | |   ||| |    |||     ||||  || |    |  |     || ||        |||    || || ||  | |||||||||||||| |||||||| |||||||| || ||||| ||||||||||||||| ||||||| || || || || |   ||    |||  | ||| |  |
gtaaaaaagacagaactct-taatgatttga-gctttatga----ttgtgtagtttggtctgttttttaaggtggggttctct----gttgttgtgtttgtgtg--ttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT

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|32245929|gb|CD711748.1|CD711748
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|46918304|gb|CN547633.1|CN547633
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTTTTTGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110384620|gb|EC949072.1|EC949072
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110387216|gb|EC951866.1|EC951866
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110377043|gb|EC942103.1|EC942103
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|71880359|gb|DT029414.1|DT029414
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|34550777|gb|CF518995.1|CF518995
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTTTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTACAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110718444|gb|EE095285.1|EE095285
EST:     CTGTTTGTGTANAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAA                         GTGAACCATGAGGACTTCAACGAAAGTATAATTCAAGTACAGGCCCAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|27585610|gb|CB008305.1|CB008305
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|71878498|gb|DT027553.1|DT027553
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|71878266|gb|DT027321.1|DT027321
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110426596|gb|EC993010.1|EC993010
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|33408222|gb|CF213849.1|CF213849
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|45771197|gb|CN007049.1|CN007049
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|30128623|gb|CB913962.1|CB913962
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|30252313|gb|CB969864.1|CB969864
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTTTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|30252322|gb|CB969873.1|CB969873
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTTTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|83275987|gb|DV939995.1|DV939995
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110405468|gb|EC971009.1|EC971009
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|30300725|gb|CB977519.1|CB977519
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTTTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110722804|gb|EE099394.1|EE099394
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|110375176|gb|EC940137.1|EC940137
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|34543899|gb|CF512131.1|CF512131
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTTTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTCCAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
EST: gi|71877789|gb|DT026844.1|DT026844
EST:     CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAG                         GTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG
genomic: CTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctc ... ttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT
                     tactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcaa