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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG

Basic information

species Vitis vinifera
transcript Vv04s0069g00800.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttc---tgaaatgttt--tatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
  || |  | || ||   | ||||| |  |    |   |  ||||||   |||| |   |||     |||  |  | ||||   |||  |||||  | | |||||||| ||||||||  | | ||||||||| | ||| ||||| |||||||||||||| || |||||| |||||||||||||||| |||||||
--aattcatagtcta---tatggagcagtaatgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 2
ttaagtttttgtttaaggtttggagtaacacc-attgagtccattatgcaggcaatttttatttcagaatttct-taattttctgaaatgttttat-gtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
     ||  ||  | |   | |  ||| | |   |    |   ||||   | |  |     | |     ||  | ||||||||     | ||||    ||||||||||||||||| || | |||||| || | ||| |||||||| |||||||||   || |||||  | |||||| | ||||| |||||||
---tattcctgactcaatatagtggtaccccttgtactataagttatttggacgttgcgggtatgtttgttgatgtaattttcaagtgtatttttccatgcagTGTCTGGGTTGCCCGTAAACCACCTGGTTTTGCATTTATCGATTTTGATGACAAGAGGGATGCTGAGGATGCACTCCGTGATTTAGATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G027105_T02 (Zea mays), 3'ss of exon 2
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgtt--ttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG-----------
  |||   | || |     |       | | || |   |   |     ||   ||| |  |||      ||     |   ||||  ||||  ||   |||||||| ||||||||  | | ||||||||| | ||| || || |||||||||||||| || |||||||||||||| ||||||||||| ||||           
-caagaaat-gtattgaactcaataccatatcactttttttgtacaatagattattatagtttatatgctttcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATGGTACTTAATAA

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G027105_T06 (Zea mays), 3'ss of exon 1
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgtt--ttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
  |||   | || |     |       | | || |   |   |     ||   ||| |  |||      ||     |   ||||  ||||  ||   |||||||| ||||||||  | | ||||||||| | ||| || || |||||||||||||| || |||||||||||||| ||||||||||| ||||
-caagaaat-gtattgaactcaataccatatcactttttttgtacaatagattattatagtttatatgctttcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G107896_T01 (Zea mays), 3'ss of exon 2
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaatttt-ctgaaatgtt--ttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
  ||| | |||       |        | |   ||   ||  |     ||   ||| | |||| | |     | | ||   ||||  ||||  ||   |||||||| ||||||||  | | ||||||||| | ||| || || ||||| |||||||| || |||||||||||||| ||||| || || ||||
--aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgt-attttatatgcattcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
ttaagtttttgtttaag--gtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaat--ttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
    |||||||||  ||  ||||  | |       ||   || | || |       |||| |    | |||  || |   |||  ||  ||||| | | |||||||| ||||||||||| |||||||| || ||||||||||| |||||||||||||| ||||||||||| ||||| || |||||||| ||||
--cggtttttgttgcagtggtttttatttgttttgtttt-tctaataggtctatt-ttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
---------ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
          |  | |||| |||   |||| |  |   || |||  ||  ||| || |   || |   ||||     ||  |   |  |     ||||| | | |||||||| ||||||||||| |||||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| || |||||||| ||||
gttttgttgctgtgattttattttttgttttg--ttctactattaggtttattttgaaaaaaaatg--attttgtgtttaatgggtact-----atgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S207_102V6.2 (Physcomitrella patens), 3'ss of exon 1
ttaagtttttgtttaaggtttggagtaacaccattgagt--ccat----tatgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
  | | || ||  |     |   | | |||  || ||||   |||    ||||     |||||   | | | |  | ||    | |||||  | |      | |||||| ||||| |  |||| |||||| |||| |||||||||||| ||||| || || ||||||||| | ||||| |||||||  ||  |||
cgatggttgtgagttcaactc--actgacaagatggagtattcatgttgtatgttaagaatttgcttctgaaagctactcg--tgtctgacttat--ggatttcagTGTATGGGTCGGCCGCAAACCACCGGGCTTTGCTTTTATCGAATTTGAAGATCGAAGAGATGCAGATGATGCCATTCGTGCCTTGAATG

upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S332_29V6.1 (Physcomitrella patens), 3'ss of exon 1
--ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
  ||  ||    ||     || |    |   |  | ||    | || ||     ||  | |  | | |||   | |   | |||||    |      | |||||| |||||||  |||| ||| || |||| |||||||||||| ||||| || || ||||||||| | ||||| |||||||  ||  |||
agttctgtcccagtgattcgtctctcatgcaaggactgtcctccttttgtcttgaaaatctgctgctgaaagccattcctgtctgacccat--ggatttcagTGTGTGGGTTGGCCGCAAACCGCCGGGCTTTGCTTTTATCGAATTTGAAGATCGAAGAGATGCAGATGATGCCATTCGTGCCTTGAATG

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|37190703|gb|CF610052.1|CF610052
EST:     ACTGAGCGAGAACTTGAAGATGAGTTTCGTGTTTTTGGAGTTATAAGGAG                         TGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGA
genomic: ACTGAGCGAGAACTTGAAGATGAGTTTCGTGTTTTTGGAGTTATAAGGAGgtataacaat ... ttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG
                         tcttaat  putative branch site (score: 3)
       aatttttatttcagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - ggtttgg
- - - - - - - - - - - - - aacacca
- - - - - - - - - - - - - - - - - - - - - - - gcaggca