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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctgaggttttaacggggtttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG

Basic information

species Vitis vinifera
transcript Vv07s0005g00740.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G37420.1 (Glycine max), 3'ss of exon 2
gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctgaggttttaacggggtttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
              | ||   ||| |||||||   | | ||   ||   | | |||  ||| | ||    |||         | |   || |  | |||||||  ||||||||| ||||||   ||||| |||||||||||||||||||| ||||||||||| ||  |||||||||| || || ||||| | ||||| ||||||||| |
-------------gttagtcttct-cttctcttccttatagt--ttcattcctttttgttatattcattcatg---------ttactattgagtgtggttttt--gcagGTGGGAGATGCTGTGAAGGACCACGCTTGTTGGGAGAGACCCGAGGACATGGATACCCCAAGGAGTGTCTTTAAAGTAGATAAAAACAACCCTGGTTCTG

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 2
gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctgaggttttaacggggtttt---tctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
             |   ||  | |  |     |  |  |   |||   ||  |       |  |  |||  || |          |||||     || ||||   | |||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||| ||| |||| || || || ||  ||||   |||||| ||||||||||
------------ttatggaaattttttaaaaaaaatggggttagtcttctttagggagagaatggggaacttgaattctgatattggtttggtttggtttttggctttgcagGTGGGGGATGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGATACTCCAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 2
------------gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctg----aggttttaacggggtttt------------------tctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
                    | ||  | | |||      |  |  ||| | || |  ||   | |  |  ||    || || |||  |     ||     || || | |      |||                  | |||||||||| || ||||| ||||| || ||||||||||||||||||||||||||||||||   ||| || || || ||  ||||   |||||| ||||||||||
gtcagttaagacaacaacactcttgctaaaatcaacttatacccttttgaaagtaactatggaaaagttttttttttcaaatatggggtaagtcttctttagattctgatatttgtttgtttgtttgttattgggctttgcagGTGGGAGACGCTAAGAAGGACCATGCTTGTTGGGAGAGACCAGAGGACATGGACACACTAAGAAGCGTGTTTAAAATAGATGCAAACACACCTGGTTCAG

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G40030.1 (Glycine max), 3'ss of exon 4
gtt--ttgtgttttcttcagatctctgcttctct-atttcagagcagtta--cctacatttgattagagt--cgaaaatgcagaggagctgaggttttaacggggt---ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
|||  |  | | ||| | |    |    |||| |  |||  |    ||||  | || | |  ||  |  |   || || |||  | |  |   ||| |     | |    ||| |||||||||| ||||||   ||||| |||||||| ||||||||||| ||||||||||||||  |||||||||| || || ||||| | ||||| ||         
gttagtcttctcttcctaatgctttcatttcttttgtttttgtcatgttatgcataaaatgcatatggctactgagaaagcaaggtaaatattgttattgttagttgtggtttttgcagGTGGGAGATGCTGTGAAGGACCACGCTTGCTGGGAGAGACCCGAGGACATGGACACCCCAAGGAGTGTCTTTAAAGTAGATAAAAACAACCTG-------

upper sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctgag-gttttaacgg-ggtttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
                     | |  | || |  |  | |    ||  || |     |  | |    || |    | | | | ||| | |||||||   |  | |    |||| |||||| |||| | ||| || |||||||||||||||||||| |||||||||||  |||| ||||| || || || ||||  ||||  |||||||| |
--------------------gttttttactttgctctaaa----ttctctcctcgaaaaaaaaaaacaagactttgggaaacagagtggtttaacgttagcgtgttcatagGTTGGTGATCCTAACATGGACCATGCTTGTTGGGAGAGACCAGAAGACATGGACACACCAAGAAGTGTGTTTAAAGTCGACAAGAACAATCCTGGTTCTG

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|349828703|gb|FQ418438.1|FQ418438
EST:     CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAG                         GTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAGgttttgtgtt ... ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|351029054|gb|FQ435254.1|FQ435254
EST:     CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAG                         GTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAGgttttgtgtt ... ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|161715260|gb|FC065809.1|FC065809
EST:     CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAG                         GTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAGgttttgtgtt ... ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|110700767|gb|EE077711.1|EE077711
EST:     CCGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAG                         GTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAGgttttgtgtt ... ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|351043975|gb|FQ431406.1|FQ431406
EST:     CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAG                         GTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAGgttttgtgtt ... ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
EST: gi|71877408|gb|DT026463.1|DT026463
EST:     CCGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAG                         GTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG
genomic: CTGATTACCTCCTCAAAGCCACTGTCCATCCAGACACCATTTACGTTCAGgttttgtgtt ... ttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattagagtcgaaaatgcagaggagctgaggttttaacggggtttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG
                                 ttttaac  putative branch site (score: 2)
                                            tttttctgc  putative PPT
                                 ttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgtgttttcttcagatctctgcttctctatttcagagcagttacctacatttgattagagtcgaaaatgcagaggagctgaggttttaacggggtttttctgcagGTGGGTGATGCTAATAAGGATCACGCTTGTTGGGAGAGACCAGAGGACATGGACACTTCAAGGAGTGTTTTCAAGGTAGACAGAAACACCCCTGGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG