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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttctccgatcattcttctgtaatagattttaagattttcccaaaaaacattagttcttgacttatgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA

Basic information

species Vitis vinifera
transcript Vv17s0000g01530.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------tatttctccgatcattctt------ctgtaatagattttaagattt--tcccaaaaaacattagttcttgacttatgaaccatgcctttgc------attttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
                                                                   || | ||  ||| |  |||       |  || | | |  |  |||   |   |||   | ||  || || ||||    | ||     | |       | | |||    |   ||| |||||||| |||||||||||||| || || ||||| ||||| || || |||||||| ||||| |||||  | || ||||||||||| 
gtatgttgtgttgatctaactggaaggaagtcatacttaaaatactacttgctaagtttatgataaataatgcta-gataagccttgaaagttttcaacacactggacaattcaatgttaaattgcttttctttttcacttgcccaacacattctggtgacaaaactgtatttactttaagGAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAG

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G099547_T03 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------tatttctccgatcattcttctgtaatagatttta----agattttcccaaaaaacattagttc---ttgact--tatgaaccatgcctttgca---ttttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA-----------
                                                                                |   |   |   || | |  ||| | | ||| ||     ||  ||       |  |||  ||    || |||  |    || |||  ||  ||   || | |    |  |||| |||||||| ||||| |||||||| || |||||||| | ||| || || ||||||||||||| |||  |  | ||||| ||||||||            
gtatgcattttttaacaatgtagtatgctatcttttttttgaaactacaacatgcaatgtttatgatgaaaagttgtacatggctgcactgacagtttcatgtgaaacattgtagattggacattggtgtgcactatttctttgagttcactggtgcatacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGGTGATTTTCTT

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G099547_T04 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------tatttctccgatcattcttctgtaatagattttaagattttc-ccaaaaaacattagttctt------gacttatga--accatgcctttgc---attttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
                                                                                |   |   |   || | |  ||| | | ||| ||   |   |         || || |||||       |||  ||   || |||  ||  |   ||| | |    |  |||| |||||||| ||||| |||||||| || |||||||| | ||| || || ||||||||||||| |||  |  | ||||| |||||||| 
gtatgcattttttaacaatgtagtatgctatcttttttttgaaactacaacatgcaatgtttatgatgaaaagttgtacatggctgcactgacagtttcatgtgaaacattgtagattggacattggtgtgcactatttctttgagttcactggtgcatacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G63440.1 (Arabidopsis thaliana), 3'ss of exon 4
tatttctccgatcat--tcttctgtaatagattttaagatttt-cccaaaaaacattagttcttgacttatgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA-----------
          | |||  | || ||  | | | | ||   | || | ||    ||||   |  | || | |  ||   |||| |    |||| ||      ||||||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || ||| ||||||||||||| |             
------gtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaat--tgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGGTACCAAATCA

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
tatttctccgatcat--tcttctgtaatagattttaagatttt-cccaaaaaacattagttcttgacttatgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
          | |||  | || ||  | | | | ||   | || | ||    ||||   |  | || | |  ||   |||| |    |||| ||      ||||||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || ||| ||||||||||||| |  
------gtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaat--tgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S121_20V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------tatttctccga-------tcattcttctgtaatagattttaagattttcccaaaaaacattagttcttgactt-atgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
                                                    | |||||| ||       || |     || ||| | ||    || ||| |   |   |     || | || |  |||||    |  ||  |         | ||| ||| |||||||| |||||||| || || ||||| ||||| |||||||||||||| ||||| ||||| || ||  | || | |||||| || 
gtatgttctcctacacattaattttatctaaatttcacgttgatgcttgagatttttctctgaagaggaatcctctcaatgcaat-gcttccgtgactttgcgttagggctcggcttgtggattcgatgaagacagtgttgacgacagtgtgtttac-agGTGTGAATGCGGATGATGTCCGGGTAACTGTGGCTGCACCTGCAGCCCGTGGTGAAGCAAACAACGAGCTGCTTGAGTACATGGGGAAG

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|351012338|gb|FQ430023.1|FQ430023
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA                         GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
EST: gi|351029663|gb|FQ427503.1|FQ427503
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA                         GGGTGAATGCAGACGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
EST: gi|349821093|gb|FQ404346.1|FQ404346
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAGTTACAA                         GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
EST: gi|351027269|gb|FQ444518.1|FQ444518
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA                         GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
EST: gi|351040562|gb|FQ438106.1|FQ438106
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA                         GGGTGAATGCAGACGATGTTCGAGTGACTGTAGCTGCGCCTGCGGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
EST: gi|351027068|gb|FQ439929.1|FQ439929
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA                         GGGTGAATGCAGACGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
EST: gi|351019261|gb|FQ429421.1|FQ429421
EST:     CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA                         GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG
genomic: CCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAAgtaaaatatt ... catataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaacattagttcttgacttatgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
            tcttgac  putative branch site (score: 3)
                                       ttttatc  putative PPT
                                      attttatcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttctccgatcattcttctgtaatagattttaagattttcccaaaaaacattagttcttgacttatgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- tttctcc
- - - - - - - - cttctgt
- - - - - - - - - - - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaac