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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttccaggtcttttgctagagaggttggtggtttttttctcatgttacatcatataacgtgcttctttgtgactacaaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC

Basic information

species Vitis vinifera
transcript Vv18s0001g01620.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 14
----------------------------------------cttccaggtcttttgctagagag---gttggtggtttttttctc---atgtt---acatcata-taacgtgc--ttctttgtgactacaaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC
                                           | |  | | ||    || |        |    ||  | |||   | ||    | || ||  |  | |||  || |||     |  ||  | |||   | ||| | ||||||||||||| ||||| || ||||||||| | || || |   | |||||||| || || ||| |||||||||||||||| ||||||||||| || ||||||
gtaataagttttccctagcgtaggtatcactctctaccagtaactatatttattaacggacaacaaacatgcaaattactactctagaggtctaaagatgatgctgccttgctgttttttacatttgaaaggtttttgatgttatttttcagCCTTGCTGTCTTGGAAGGCATTGCAATCAGCTTCAATCCCAACTACAAAGTCTTGGGCAGTTCATACCCATGGATTGCAAGAAAAGTTCTCACAGACAGC

upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G305007_T01 (Zea mays), 3'ss of exon 14
------------------------cttccaggtcttttgctagagaggttggt-----ggtttttttctcatgttacatcatata-acgtgcttctttgt-----gactacaaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC
                           | | ||  ||  |||     | | |      ||    |     |   ||| ||  |||    || |   | ||      | ||  |    |     |  || | |||||||||||||||| || || || |||||| | || || | | | || |||||| | || ||| |||| ||||||||||| ||||||||||| |||||||| 
gtaatgagtttgtctgcaaaatttgagcaaagtgcttcactaattgagcttgcaaccaggcagatgctctagagtacctctgatatgtatgttctctggttcatcaaataagaggcttaccatgtgatttttcagCCTTGCTGTTTTAGAAGGTATCGCAATCAGCTTCAATCCAAAGTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGT

upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 14
cttccaggtcttttgctagagaggttggtggtttttttctcatgttacatcatataacgtgcttctttgtgactacaaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC
                   || ||||         || ||      ||| |  |||| ||   |        ||| | | | | ||| |   ||| | |||||||||||  |||| |||||||||||| | |||||||  || ||||||||||| |||||||| ||||| ||||||||| ||||||| || ||||||| |
-----------------gtagcggtttcca-cacattacttgcaacacaaccaataatgtctgtgcaaaatcctaaacagtatcttctg---tcttttagCCTTGCTGTACTGGAAGGAATTGCAATCAGCTTTAACCCTGAGTACAAAGTTTTGGGTAGTACTTACCCTTGGATTGCTCGAAAAGTACTTACTGACAAC

upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 13
cttccaggtcttttgctagagaggttggtggtttttttctcatgttacatcatataacgt-gcttctttgtgacta--caaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC
 |  || ||  |   | |    || |  |   |  ||   ||| ||   ||   | | |  || |     | | |       ||||  ||     |  | ||| ||||||||||||||||| ||||| |||||| | | || | | ||||| ||| |||| ||||||||||| ||||||||||||||  ||||||| ||||||
ttggcaagtactcaaccac---ggcttatatgtgattagccattttctgtctactgaggcagcattcacataattttttggcttctcatctttggttccccagTCTTGCTGTTTTGGAGGGCATTGCCATCGGTATAAGCCCAAACTACAAGGTTCTAGGCAGTACATACCCTTGGATTGCTAGAAAGATTCTAACCGACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcatataacgtgcttctttgtgactacaaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC
      atataac  putative branch site (score: 3)
                                  ttcttttccgctatct  putative PPT
                               aaattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttccaggtcttttgctagagaggttggtggtttttttctcatgttacatcatataacgtgcttctttgtgactacaaattcttttccgctatctctcagCCTTGCTGTTTTGGAGGGAATTGCAATCGGTTTTAACCGAGATTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- -ccaggtc
- - - - - - ttgctag
- - - - - - - - - - - -gttggtg
- - - - - - - - - - - - - - - - - - - ctcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct