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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG

Basic information

species Vitis vinifera
transcript Vv09s0054g00700.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 7
--atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
  |  ||  || | |        ||  | |  ||    || | |||         ||||   | | |  | | ||  ||| | |           |    ||||||| ||||||||||| |||||||| ||  |||| ||||| || ||||| || || ||||||||||| |||||||| |||||||| || ||||||||||
agagatgcatc-tcgaaaatcactttgtattattattattatcctattatgctc-tgtaacacatgtatacatcagtagtatactaaaagagggctactcagGTTGGTGACAATGTTGGAGATTGTGCCGCACGAGGGGCTGACCTTTTTGAGAGCATAGCAGCTGAAATTATCAGTGCAATGATACTCGGGGGAACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 7
atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttca-----tttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
   | |||| ||| |  |    |    |  ||||||| ||  |        |  ||   || ||| | ||  |    || |       |   |     |    ||||||| ||||||||||| |||||||||||  |||| |||||||| ||||| || || ||||| ||||| |||||||| |||||||| || ||||||||||
-aatatttctttgctctacaactt---tacttgccttgttcttgttatcctatagttcatcttttgc-tactatatattcttgtataacaaaagaaactactcagGTTGGTGACAATGTTGGAGATTGTGCTGCCCGAGGCGCTGATCTTTTTGAGAGCATAGCAGCAGAAATTATCAGTGCAATGATACTTGGAGGAACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
-------atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
       ||||  || | | ||||  ||||  | ||||||  | |  | |    |         ||| ||| |  |   |      |    |    || |||| |||||||| |||||||| || |||||||||||| ||||||||||||| ||||||||||||||||||||||| |||||||| |||||||| |||||||||||||
gtttataatttccttgacttgtgc--tttttgtttctttgtttatactttttctggt-----cttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
atttgtttcattggtgcattt-ttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
||||  || | | |||| ||| ||  | | |||    |||||||      | |  || | | ||| |  |   |      |    |    || |||| |||||||| |||||||| || |||||||||||| ||||||||||||| ||||||||||||||||||||||| || ||||| |||||||| |||||||||||||
atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagt-tatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------------atttgtttcattggtgcatttttcatgtctttgccttttttc---taagggaaaaatgtatgtcctttccataacaagagtttt----ccctcttcttcat-ttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
                                          | || |||      |     | | ||| |  | | | | ||     |        ||  |||  ||||   |   ||   |||    || | ||| || | ||| |||||||||||||||| || || ||||||||||||||||||||| | ||||||||||| || || |||||||||||||| |||||||| |||||||||||||
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 8
atttgtttca-ttggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
    || | | ||  | |||||  |    |||||  | |  | |    |      | |  |  | ||   |   |   ||  | ||| |||||  ||| ||||||||||||||||||| || || |||||| ||||||||||| | ||||||||||| || || |||||||||||||| |||||||| || || |||||||
----gtattagttctttcatttcacgatcctttgtgtatgattttgtcgggcctggaaccttttgtcatcactgaagcttcactctcatcttc--ttgcagGTTGGAGACAATGTTGGGGACTGCGCTGCTCGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTTGGGGGTACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------atttgtttcattggtgcatttt-tcatgtctttgccttt--tttctaagggaa------aaatgtatgtcctttccataacaag---agtt-ttccctcttcttcatttga--agGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
                                                    |||  ||||  | ||  | |  || | ||| | | |    | || ||  |||      |||  | |      || ||    ||   |||| ||    | | | |||| ||  |||| |||||||| || || |||||||||||  | ||||| ||| | ||||||||||||||||||||||| |||||||| ||||| || ||||| || ||||
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------atttgtttcattggtg-catttttcatgtctttgcctttttt----ctaagggaaaaatgtatgtcctttccataacaagagttttccct-cttcttcatttga--agGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
                                                || ||  | ||||| || || |  ||| || | |  |  |     | |   | |  ||  |  |  |           ||||     | | | | |||   |  ||||||| || || || || |||||||||||  | ||||| ||| | |||||||||||||||||||||||||||||||| ||||| || ||||| |||||||
gtatgctcaaattaatgttattctgtatatgtagttgtctaattttgattattagactggtgtcagttgtagtgtgttggacactagtagagttcatccacatttgagtacctctattggtcttccagttgctgatgcctgtacatcgaagtagGTTGGTGATAACGTGGGAGATTGTGCTGCCCGTGGTGCCGATTTATTTGAAAGTATTGCAGCTGAAATCATCAGTGCCATGATTCTTGGTGGTACAATGG

upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ13082 (Selaginella moellendorffii), 3'ss of exon 6
atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
                                               | ||| | | |    |     ||      |   |   |  ||||       |||||||||| ||||||||||||||||||||| | ||||||||| | || ||||||||||| || || || || || || ||||| ||||| || || ||||
-----------------------------------------------gtaaattttgtagtttacgtttagttgatggacttaatggtctt-----acagGTTGGAGATAATGTTGGTGATTGTGCTGCTCGTGGTGCTGATTTATTCGAAAGTATTGCTGCGGAGATAATTAGCGCCATGATTCTGGGAGGCACTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
                    ccataac  putative branch site (score: 3)
                                ttttccctcttcttca  putative PPT
     aaatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - -gtgcatt
- - - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - -tgccttt
- - - - - - - - - - - - - - - - - - - - - - - ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaga