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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA

Basic information

species Vitis vinifera
transcript Vv08s0007g06680.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g53380.1 (Oryza sativa), 3'ss of exon 1
atcctgttgtgttgt-atttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcatt-cagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
       || ||||  | |  |  |   |  ||| |  ||  ||||   | |  |   | ||   |||   ||   ||| || |  ||    | |||  ||| |||||   |||| | ||||||||   | ||||||| ||||| ||||| ||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| 
------gtgagttgagactacttgagcaactctgttttattcagttcttggtgtttcatgtgacacagc--tgaaaattcagttccatgatgttcataacagATTGAACCCGAGTGACATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTCGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGGTTTGCATC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g10560.1 (Oryza sativa), 3'ss of exon 1
atcctgttgtgttgtattttta-taatgaaactgatccatctagtttaagttcctgggtttgttccagtg-atgttg-atttagatgaattgattgcat-tcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
        |||  | |   ||| ||  | |    ||| || | | | || ||      |   |   |||| ||        ||  |  |||  |   || | || ||||||   | | ||||||||||   | ||||||| || ||||||||||| || || ||||| || |||||||| ||||||||||| ||||| ||||| 
--------gtgaggaaaagttactagagcaggcaatcaattttggtgaattttt--attccatcttagtgcataacatgcctaattatattcttgttatattagATTGAATCCAACTGATATGTTGGAGAGGCTGAGGGGGAAAAGACTGGTTTTCGTTGGTGATTCACTTAATAGGAACATGTGGGAATCCCTGGTCTGCATC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G843892_T01 (Zea mays), 3'ss of exon 1
--------atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcat-tcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
            | |  ||    |  |      |  |  |  | || | | |  | ||||   | |   ||    |  ||    ||||| |   |    ||  | | || |||||    | | ||||||||||   | ||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||||||||| ||| |||| || 
gtgagaaaggtttatactgcaacaactacgcggtttagttactgcaccaaatgca-gttctgtgttgctttttttttttgaaagtttagttctgtcatctgtgtgttagATTGAACCCAACTGATATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTGGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGATTTGTATC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G165961_T01 (Zea mays), 3'ss of exon 1
-------------------------------atcctgttgtgttgtatttttataatgaa--actgatccat--ctagtttaagttcctg--ggtttgttccagtgatgttgatttagatgaattgattgcat---tcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
                                |  || ||  ||  ||  ||||| | |   | ||     |  | | |  |  |   ||  | ||| ||  |  | | ||  ||  |     |   |||| |   | ||||||||    | | | ||||||||   | ||||||| ||||| ||||| ||||| || ||||| ||||| ||||| ||||||||||| ||| |||| |||
gtgagaaaaaaagtacttcaacaactgcgccgttttggtgaattcaatagttatagttagttattggcgtgtgacaaatgcagttctgtgttgctttattttaaagttattagttctgtcacctgtgttgcttatgttagGTTGAACCCAACTGACATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTCGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGATTTGTATA

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G033805_T01 (Zea mays), 3'ss of exon 1
atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
 |   | |  | | || |   | |||| ||  | |  |  || || |  || |    || |||       |||  | ||  |||  |   |    ||||| |||||    |   ||||||||||   | |||| ||||| |||||||| || || || ||||| ||||||||||| ||||||||||| || || || || 
gtgaggataaggt-tactggaacaatgcaatggttttaattatttca--tttcaatcttggtttgtaatttgtcaagttc-atgtttgtgtcat-ttcagATTGAACCCAACCGATATGTTGGAGAGGCTGAGAGGAAAAAGACTGGTGTTCGTTGGTGATTCGCTCAATAGGAACATGTGGGAATCCCTTGTGTGTATT

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G30210.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------atcctgttgtgttgtattt-ttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgtt---gatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
                                                                 ||  || |    || |||| || |  || |    |      | | || | || ||   ||| ||   | |         |||| | ||||||| |   ||  |||||| ||| |  ||  ||| || || ||||||| || ||  ||||||||||||| || ||||| ||||||||||| |||||||| ||| || ||||||||
gtaaagtttttaacttcatgggtgtttatgtttttgtccaaaattgacaatattttgtctattttattttggtaatgtgaatttgttgtcttgtattatacttgaattgattcatttgctaattttcttttggggggtcccaaaatttggttgaattggtaatat--agGTTGGATGCGCATCGAATGCTGCAATTGTTGAGAGGGAAACGACTGGTTTTTGTTGGCGATTCGCTCAATAGGAACATGTGGGAGTCTTTGATTTGCATA

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G16780.1 (Glycine max), 3'ss of exon 3
-atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
  | || | ||    |  ||| ||           ||  |    |||  | |||| | ||||||    || | |    || | |    | |||||   ||||||| ||||   |   ||| ||||  ||||||| || ||||| ||  ||||||| || |||||  |||||||||||||||||||||||||  ||||||| 
gtttctttagtaccttgctttaattgctgttgcattctcttgttttttggatcctag-tttgttgatttgctataatatttgttcgtgtaattgctaacagGTTGGATGGACATATAATGCTGGATATGTTGAGAGGCAAGAGGCTAATTTTTGTTGGTGATTCCATCAATAGGAATATGTGGGAATCTCTAATTTGCATC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G28840.1 (Glycine max), 3'ss of exon 3
atcctgttgtgttgtatttttataatgaaactgatccatctagtt--taagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
 |  |  | || | | ||    ||||  | |   ||  | |  ||  |  | |||| | ||||||    || | |    || | | |  |  ||||    |||||| ||||   ||  ||| ||||  ||||||| || ||||| ||  | ||||| || |||||  |||||||||||||||||||||||||  ||||||| 
-tgtttctttggtattttgccttaattgatccattctctttgtttctttggatcctag-tttgttgatttgctataatatttgttcatgtatttgctaatagGTTGGATGGACATCGAATGCTGGATATGTTGAGAGGCAAGAGGCTTATCTTTGTTGGTGATTCCATCAATAGGAATATGTGGGAATCTCTAATTTGCATC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATAT-GTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
             ||   |||     | ||| | ||  || |  || | |   | |  ||    |  |||  |  | |   ||  ||  ||    |  ||||| ||||| ||  |||| ||||||  || | || ||||  ||||| || |||||||| ||||| || |||||||| |||||||||||||||||||| || 
-------------gttagttttggtcggaacagttc--tcaaaatttaatatttagccttaaggctctgaaatctaat--aatagatcaat-atgtgaagGTTAAATGG-AGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT

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|71861366|gb|DT010421.1|DT010421
EST:     AGCCAAAAGGCTGTGATTTACCCAG                         GTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTT
genomic: AGCCAAAAGGCTGTGATTTACCCAGgtgcggtagc ... ttgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTT
EST: gi|71863998|gb|DT013053.1|DT013053
EST:     AGCCAAAAGGCTGTGATTTACCCAG                         GTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTT
genomic: AGCCAAAAGGCTGTGATTTACCCAGgtgcggtagc ... ttgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA
                                       aattgat  putative branch site (score: 4)
                           ttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATATGTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA

- cctgttg
- - - - - - - - - - - -aatgaaa
- - - - - - - - - - - - - - - - -atccatc
- - - - - - - - - - - - - - - - - - - - - - - - -ttcctgg