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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG

Basic information

species Vitis vinifera
transcript Vv01s0026g00310.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 5
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtg------gtttcatgacatgcta----cattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
         | ||  ||||||    ||| |||  ||    |   |  | |       |       |||||       | | ||  |    ||    |||| | |||| |||| |||||||||||||||||||| || || || || ||||| ||||| |||||||||||||| ||||| ||| |||| |||| ||||||||| |||||||
---------gttga-attattcttttagtaaaccatgttttttgttgaagtcttctttcccgcagctgtgctctgtatcttatatcgaattatttgcattgcatttccagGTTGCAACAAAAACTGAGTCAAATAAGAACGCAGGAAATGCTATTTTATATGAATGTGTTGAGACTATAATGGGCATCGAAGCTACTAGTGGTTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g56110.2 (Oryza sativa), 3'ss of exon 5
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttc--atgacatgcta-------cattccttt-tctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
              ||  ||||  | | ||   | | |  ||  |   |     || ||   ||  | | |||    |||  ||  ||        |||  ||| |  |||| ||||| |||| ||||||||| || |||||||  ||||||||| |||||||||||||| | ||||| ||| | ||||||| ||||||||| |||||||
----------tatttaaaattttacaacaatgcacttctttgtttttgtaattgaacttgttttcatattgttgtggatggaatattaaccatggtattgttttgtgcagGTTGCAACGAAAAATGAGTCAAATAAGAATGCTGCTAATGCCATTCTGTATGAATGTGTTCAGACTATAATGGGTATTGAAGCTACTAGTGGTTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G054210_T01 (Zea mays), 3'ss of exon 5
---------tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
          | | | |   |   |||||||| | |   | | ||     | |||      ||   | | || |||    || ||        ||   |  || || |||| ||||||||||||||||| ||||| |||||||| || |||||| |||||||||||||| | ||||| ||| | ||||||| ||||||||| |||||||
tataataccatggagtagtttttcattatttaaccaatgacagatgtatggtatatgc---catgttgtgctgactaaacttgca------attattatttttatccagGTTGCAACAAAAACTGAGTCCAACAAGAATGCTGGAAACGCCATTCTGTATGAATGTGTTCAGACTATAATGGGTATTGAAGCTACTAGTGGTTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G017421_T02 (Zea mays), 3'ss of exon 5
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatgg-acaaagttta-cttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
       ||  |  || | | |||           |   || || |  ||| |     |||| |||    ||| ||    |||  | | ||| |||||| ||||  ||||||||||||||||||| || |||||||| ||||| ||||| |||||||| || || || || ||| ||||||||| ||| ||||| |||||||
-catcttatctttgtagtttgtactcttttttgggttatcttcacacttggcattccctttatctttgcatggattataaacacacga-atttcttttccagGTTTCAACAAAAACTGAGTCAAATAAGAATGCTGGAAATGCTATTTTATATGAATGCGTGGAGACAATAATGGGCATTGAAGCTACAAGTGGTTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G030144_T01 (Zea mays), 3'ss of exon 5
--tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
    |    ||  |    || |  || |        || |  ||||        |    ||  |||  ||||| ||    |||    | ||| |||||| ||||  |||| ||||| |||||||| || |||||||| ||||| ||||| ||||||||||| || || || ||||||||||||| ||| ||||| |||||||
atcatcattatcttatctttgtacactttttgggttat-ctttgcacttggcatcccctttatctttgtgtggattatgaacacatga-atttcttttccagGTTTCAACGAAAACCGAGTCAAATAAGAATGCTGGAAATGCTATTTTATATGAATGTGTGGAGACAATAATGAGCATTGAAGCTACAAGTGGTTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 5
--tttgtgcatgctgctattatttacctagaaaaaaatac-gctgcataaatggacaaagtttacttactg-tggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
  | || | |      | ||| |   |||      | ||  | ||   |  |   |  |  ||    |||| |  |||    || |||| |    ||  | |||||||| ||||| ||||||||||| |||  ||| |||||||||||||| |||||||||||| |||| || |||||||||||||||| | ||||||||||||
tatgtgagtaaatgaattttaatctactattgcttattattggtggtcatctcttcggaaattcaagactgataatttttacacttgctgc----ctggtttagGTGGCTACAAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
-tttgtgcatgctg--ctattatttacc-tagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
 | ||||  |  ||   | | || |||  | |   |   |  |  ||           || ||||       |  |||    || |||| |    || || |||||||| || || ||||||||||| |||  ||| |||||||||||||| |||||||||||| |||| || |||||||||||||||| | ||||||||||||
ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgc----ctgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 5
tttgtgcatgctgctattatttacc-tagaaaaaaatacgctgcataaatggacaaagttta-cttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
  || |    |   | | ||||||  | |   |  ||  |   |  |  |         |||  |||  || | ||  | | |      ||| |||||  ||||||| ||||| | ||||||||| |||| |  |||||||||||| || ||||| |||||| |||| || |||||  ||||||||| | |||||||||| |
aatgggttgacaaatttcatttactattgcctattatcagtaaccaagtttttttccccttaatttatggttgattttttaaaattgctatttctttt--agGTGGCTACAAAGATTGAGTCAAATAAAATTATTGGGAATGCCATCTTATATGAGTGTGTTCAAACAATAATGAGTGTTGAAGATAATGGTGGCTTACGCG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 5
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatg-gacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
|||||| |   |||| | |     ||    |   | |     ||  |  |  |       || | | | | | ||| | |  || |   ||  | |  ||||||||| ||||||| ||||||||||||||||| |||||||| ||  | || ||||| ||| |||| || |||||||| ||||| | | ||||| |||| |
tttgtgaaatttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgattt-ttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ16841 (Selaginella moellendorffii), 3'ss of exon 4
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattcct--tttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
                                                         | | || |     ||  |  |        ||||  |   |   |||||||||| || || ||||| ||||| ||||||||||| || || ||||| ||||||||  | || |||||| | || || |  | | | ||  | ||||
------------------------------------------------------gtatcttctcataccagtcccgagtagaatctcatttttggctggcagGTGGCAACTAATACAGAGTCCAACAAGAATGCTGGGAACGCAATCTTGTACGAATGTGTGCAGACGATTATGGGTATAGAGGCCATTGGCGGTCTCCGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ32155 (Selaginella moellendorffii), 3'ss of exon 4
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattcct--tttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
                                                         | | || |     ||  |  |    |   ||||  |   |   |||||||||| || || ||||| ||||| ||||||||||| || || ||||| ||||||||  | || |||||| | || || | || | | ||  | ||||
------------------------------------------------------gtatcttctcataccagtcccgagtagagtctcatttttggctggcagGTGGCAACTAATACAGAGTCCAACAAGAATGCTGGGAACGCAATCTTGTACGAATGTGTGCAGACGATTATGGGTATAGAGGCTATTGGCGGTCTCCGTG

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|37183449|gb|CF602803.1|CF602803
EST:     GCCAAGGTGATGCAGATGCTAGTGACTGTATGAATGACATTCTTGCTCAG                         GTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTAT
genomic: GCCAAGGTGATGCAGATGCTAGTGACTGTATGAATGACATTCTTGCTCAGgtctgttgct ... ccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG
              tacttac  putative branch site (score: 1)
                                      ctacattccttttct  putative PPT
        aaagttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatggacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - -gcatgct
- - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - -ctgcata
- - - - - - - - - - - - - - - - - - - - - - - - -ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct