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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC

Basic information

species Vitis vinifera
transcript Vv06s0009g00410.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G458728_T07 (Zea mays), 3'ss of exon 4
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                  || || | || | | ||  |    | ||   | ||     | |   |  | || |||   ||   |   |   |   |||  || | || |||  | |  |||| ||      ||||||| || |||||||| |||||  |||| || ||||||||||| ||||| || || |||||| ||||||| | |||||| |||||       ||   | 
------------------------------------------------------------------gtcggtaaagctgtgaatcttt--ctttctttcttatcctgcgaatcaatttgactgtttta--ctggcttcttaaattaacttccgaaaaaaattgttcctttctgt----tagGTGTCCAATTGGTTCATCAATGCGAGGGTGCGGCTGTGGAAGCCTATGGTGGAGGAGATGTACCTGGAGGAGACAAAGGACCAGGACGCTGGAGGCGGCG

upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G38910.1 (Glycine max), 3'ss of exon 4
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatt-taattggattttttactttgcaaagaaac--atctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                         || ||  ||  ||  ||  | |   | |     |  ||| |          || | || ||  | |   |   | | ||  | |   |  ||   ||| |||  | ||||||||||||||||||| || ||||| || ||||| || |||||||||||||||||||||||||||||||| ||||| ||||| || || ||   |  |  | 
-------------------------------------------------------------------------taatttacacattaaag--tggttcggtaacatgaactaata-------acaacagttgtagctag--ctagcaatgtgagaggtttctgatactactctttctaatgcagGTGTCAAACTGGTTTATCAATGCCCGAGTTCGGCTTTGGAAGCCAATGGTTGAAGAAATGTACTTGGAAGAAATCAAGGAGCATGAACAAGGTAATGGCT

upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G31480.2 (Glycine max), 3'ss of exon 3
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                              | |  |||           |   | ||   | ||   ||  |    ||  |   | ||| |  |   | | || | ||     |   ||| |||  | ||||||||||||||||||| || ||||| || ||||| || |||||||||||||||||||||||||||||||| ||||| ||||| || || ||   |  | || 
------------------------------------------------------------------------------ccctggttaatatacacattaaagtggttcggtagcatgaactaataacgac--agttgtagctagcaatgtg-agaggtttctgatactctttttaatgcagGTGTCAAACTGGTTTATCAATGCCCGAGTTCGGCTTTGGAAGCCAATGGTTGAAGAAATGTACTTGGAAGAAATCAAGGAGCATGAACAAGGTAATGCCT

upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G18270.1 (Glycine max), 3'ss of exon 3
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactt--tttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                               |    |   ||  |||  |  |||  | |  ||         |||||    | ||| |   |      |||   | || |    ||| |   ||   | | |||||||| |||||||| |||||||| || ||||| || |||||||||||||| ||||||||||||||||| ||  ||||  |  |     ||||| | || |
-------------------------------------------------------------------------------ttgtatctaagttttgttttctggaaa-tattaaaaaaaa--tgaaaggtatgaatggctatggaaggtttaagacgacattgttaattaagttcataat-cagGTGTCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAACCAAACAATAGCTCTC

upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                      | || ||    |||||      |    ||            | ||   |     |||  ||      | ||| | || |||  |||           || ||  | | ||||| || |||||||| |||||||| || ||||| || |||||||||||||| ||||||||||||||||| ||  ||||  |  ||    ||||| | ||||
----------------------------------------------------------------------gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataag----------tttattata-tacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC

upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G27220.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggatttt--ttactttgcaaagaaacatctaactttttgcag-tgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                                    |   |    |   | ||  ||| | ||    | |  |    || |||  ||   ||     | | | |    |  |  ||||    |      | || |||||||||| |||||||| |||||||| |||||| ||||||||||| |||| || ||| | || | ||| |||||  |   | | ||   ||         
------------------------------------------------------------------------------------tagtaattatatatattatggaatactttcttttagcacccatgattatatataatcaaaataagtattgttaatagtatcttgtgtaaaatggatgtagGTGTCAAATTGGTTCATTAATGCTCGAGTTCGAATGTGGAAGCCACTGGTGGAGGAACTTTATTCGGAAGAAATGGATATTGAAGAAAGCAGAAAAGGAA

upper sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                                                                ||   |||||      || |||   |         | || | ||    ||  ||||   |         |  | |||   |  | |||| |   |   ||||| || ||||||||||| || || || |||||| | |||||||||||||| || ||||||||| ||||||||   || ||  |     |  ||  |||  
-------------------------------------------------------------------------------ccagtatccagaacg--cttttgttaaacatccacttttgtcagaggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA

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|32269618|gb|CD718777.1|CD718777
EST:     ATTCCGACAAACACATGCTTGCGAAACAAACGGGGCTTACGCGAAGCCAG                         GTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
genomic: ATTCCGACAAACACATGCTTGCCAAACAAACGGGGCTTACTCGAAGCCAGgtatattgta ... tgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
EST: gi|32269940|gb|CD719099.1|CD719099
EST:     ATTCCGACAAACACATGCTTGCGAAACAAACGGGGCTTACGCGAAGCCAG                         GTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
genomic: ATTCCGACAAACACATGCTTGCCAAACAAACGGGGCTTACTCGAAGCCAGgtatattgta ... tgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
EST: gi|110693884|gb|EE070506.1|EE070506
EST:     ATTCCGACAAACACATGCTTGCGAAACAAACGGGGCTTACGCGAAGCCAG                         GTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAAGCCA-TGGG
genomic: ATTCCGACAAACACATGCTTGCCAAACAAACGGGGCTTACTCGAAGCCAGgtatattgta ... tgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAA-GCCAATGGT
EST: gi|32269627|gb|CD718786.1|CD718786
EST:     ATTCCGACAAACACATGCTTGCGAAACAAACGGGGCTTACGCGAAGCCAG                         GTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
genomic: ATTCCGACAAACACATGCTTGCCAAACAAACGGGGCTTACTCGAAGCCAGgtatattgta ... tgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
EST: gi|71871047|gb|DT020102.1|DT020102
EST:     ATTCCGACAAACACATGCTTGCGAAACAAACGGGGCTTACGCGAAGCCAG                         GTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
genomic: ATTCCGACAAACACATGCTTGCCAAACAAACGGGGCTTACTCGAAGCCAGgtatattgta ... tgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
EST: gi|32268362|gb|CD717521.1|CD717521
EST:     ATTCCGACAAACACATGCTTGCGAAACAAACGGGGCTTACGCGAAGCCAG                         GTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT
genomic: ATTCCGACAAACACATGCTTGCCAAACAAACGGGGCTTACTCGAAGCCAGgtatattgta ... tgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
                                  atctaac  putative branch site (score: 2)
                                        ctttttgc  CT-rich tract
     taattggatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA