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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g11700.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
-------------------------------------------------------gactcttatgctatggtggtttaccaagtta-atctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
                                                       ||  |  | |  ||      || | | |    | ||    |   | |  |     |||   | |||| | || ||||    | |||    |    || ||||||||||| ||||| || || ||||||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||  | || ||||||||||
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaata-caactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgatt-gcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 16
---------------------------------gactcttatgctatgg--tggtttaccaagttaatctc-caaagtaactccaa-aaattccaagttttgactagcg-aaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
                                 |||  |||| |||     ||   |    |  | ||      || |  ||   | |        |  || || ||   | || | |  | | |||| |  ||| |||| ||||| |||||  | || || ||||||| |||| | ||||| ||| | || |||||||||||||| || ||||| || ||| ||||||||||||| |
gttgatatttttggcatttccctttgtaaattggacagttatcctactatatgaactgttgaaatgataaaatgaaatcgctgtgataggaaatggggcttcacaagttcacatgttttgtatcttatatttttc-agGAGGACTTCTATGCTATAGTTGACTGGGCATTCAAGCTAGATCCATTGAGTTGTATATCAATGCATGGCATAACAGATCGCTATCTTTCTGGTCAGAAGG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 16
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcga--aatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
 | |  |    | |  || |||  || ||  |  |        | |     | || | |  ||     || ||   |  |||  |      ||| |||| |||||||||| ||||| || || |||||||| || || ||||| || ||||| ||||| |||||||||||||||||||| || ||  ||||||| |||||||
-aattgtgcattcttctgttttttcatgtgcacattattgtgcagtattgcagttgccaacttccttcagtgactgaaatgttttcccccttgt-attccagGAAGACTTCTATGCGGTCGTAGATTGGGCTTATAAAATTGACCCCTTGCGTTGCATCTCAATGCATGGGATTACAGAGCGTTACCTTTCTGGACAGAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G060949_T01 (Zea mays), 3'ss of exon 4
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattct-----agGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
    | ||   ||   |   | ||  | | |  |   |    |  | | || |||    | |  |  |   ||   ||  | | |||||| || |||      |||| |||||||||||  |||| || ||||||| |||| | ||||| ||| | |||||||||||||||||  | ||||| |||||| |||||||||||||||
--tgcataatttagactaaat-actga-tgagccaagagctgagttaccaacattttgggctgcg-ttgttgagccttcacttgttttatatggttccttttcagGAGGACTTTTATGCTTTGGTTGACTGGGCATTCAAGCTAGATCCATTGAGTTGCATATCAATGCATGGACTAACAGATCGGTATCTTTCTGGTCAGAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtca---ttttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
    |||||  | ||||    |       |  | |    ||  | |    | |||  ||  |    | |   | |  |  ||   |  ||||| |||||  |||||||||| ||||| || |||||||||||||| |||||||| ||||| ||||| |||||||||||||| || |||||||| ||| | |||||||||||||
-ttccttataat-tggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagc-atttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
---gact--cttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
   || |   | ||| ||    ||  |   ||  |     |  ||  | |   || | ||   ||  || ||      || |     |  ||||| |||||  |||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||||||||| || || |||||||| ||| | |||||||||||||
atagattgagtcatg-tagaaaggcatggtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatc----tgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 16
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaa-aaattccaagttttg--actagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
    |||||  | ||    |||   | |  | | |||| |   | |     |  ||   || ||||   |||   |  |   | ||  ||| | |||||  ||||||||||   ||| || |||||||||||| |||| |||||||||||  ||||||||||||||||||| | ||||||||| ||| | |||||||||||||
-ttccttataatttgacaatttgtaacg--agtttccagatggattttggtatgttaatagatttgctgctataaagttgctttataatttctctgatttcagGAAGACTTCGCTGCTGTTGTGGATTGGGCACACAAAATTGATCCTTTATGCTGCATATCAATGCATGGAACTACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
                                                |     |    | |||   |  ||   | |  ||   | |      ||  |||| || || ||||| || ||||||||||| |||||  ||||||||||| | ||||| |||||||| ||||  |||||||| ||| | ||  |||| ||||
----------------------------------------------gtagcgtctatgtgatttcgttgacg---tctaacacaatct-----gtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG

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|7593728|gb|AW707979.1|AW707979
EST:     AGCTGGGAGCATTAAATGAATCTCTTCAGGATTTGCTTGACGGTATCCAA                         GAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGC
genomic: AGCTGGGAGCATTAAATGAATCTCTTCAGGATTTGCTTGACGGTATCCAAgtaaggtcca ... gtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG
               ttttgac  putative branch site (score: 3)
                           aaatttgtcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG

- - cttatgc
- - - - - - - ggtggtt
- - - - - - - - - - - -ccaagtt
- - - - - - - - - - - - - - - - -ctccaaa