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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagcaataacttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttcttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT

Basic information

species Vitis vinifera
transcript Vv00s0283g00020.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
agaagcaata-acttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttc-ttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT
  || || |  | |  |     |  ||| |  || |   |  ||||   | | | || |||     |  ||||   | || |   |  |     || | |||||||| |||| |||||| || |||||   ||| | | | ||||| |||||||| ||||||||||||||||| || |||||| |  ||||||||||||   
--aaccattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA

upper sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os04g32960.1 (Oryza sativa), 3'ss of exon 14
agaagcaataacttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttcttagtttga-atctttctcatttgacatgtaca---gATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGAC--AAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT---------
  || |  | |||| ||| ||| | |  || |  || ||          || |||  | | |   | | ||| ||  ||  || | |  | | ||| |||     |  || |   |     || |  |||          || |||   | |||||||| || ||||||||||||||||| |||||| || ||||| |||||             
gtaatcttttacttttttttcttacatatatataaaatc----------atgttgcatccattcatgtaagtatggcattattataacataatatgaacacctactcttttacagATTATAGGTGAGTGTCAGGGAGTTGAAGGACCTGAGTTTGAAGTATTTTACATTGACTATGGAAACCAAGAACTTGTTCCTCACAGTTGCCTGAGACCTA

upper sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 15
agaagcaataacttatttctctaataattacaagaagtctatttcagttatattgtgttcct----gtttcttagtttgaa--tctttctcatttgacatg------tacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT
            || |     |  || ||   |  |   | || || || || | ||| ||     || | ||   |  ||  ||||| | |  ||  |||      |  || | || |||| |||||| ||  ||||||||||  |||| ||||  |||||||| ||||||||||| ||||||||||||||| |  | ||||||  |||| 
-----------tttgtgcacatgctatttgtcaacacatt-ttgcacttgtactttgtaccacctagtctgttcagtcaaacttctttatgaaatggtatgggatgttgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTTCAAATGACATGTTTGAAGTATTCTACATTGATTATGGAAATCAAGAAGTAGTACCTTACTCTCAGC

upper sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 15
agaagcaataacttatttctctaataattacaa-gaagtctatttcagttatattgtgttcctgtttcttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT
|  ||   | | | |  |    |||| | | |  |  |  | |  ||  ||   |||           |   | |  ||         | ||  |||  || | || |||| |||||| ||  |||||||||| ||||| ||||  |||||||| ||||| ||||| |||||||||||||||    | ||||||  |||| 
aatagggttga-tgagatgcaaaatagtcagagtgtcgcttgtaccacctagtctgttcagtcaaacttacttctttatgaaatggtatggaattgtgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTCCAAACGACATGTTTGAAGTATTCTATATTGATTATGGAAATCAAGAAGAAGTACCTTACTCTCAGC

upper sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
agaagcaataacttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttcttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGT-CAGT
    | ||    | |  | |||||  ||  |||  |   | | |   || | |  | |  ||  |  ||  ||    | ||||  |||||   |||  |||||||||||| |||||| || || ||| |||| ||| | ||  ||||||||||||||||||| || |||||||| ||||||||  |||| |||||  ||  
----gtaaattataaagtttctaaatatgccaaccatgatttcttctttttttactatcacttatggttgtttattgtatttcgtatttg---tgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA-

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|27584247|gb|CB006942.1|CB006942
EST:     ACATTGTCCTTGCGCAATTTAGTGCAGATAATTCGTGGAACCGAGCAATG                         ATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAA
genomic: ACATTGTCCTTGCGCAATTTAGTGCAGATAATTCGTGGAACCGAGCAATGgtgagattta ... acatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAA
EST: gi|30253044|gb|CB970595.1|CB970595
EST:     CCTTGCGC-ATTTAGTGCAGATAATTCGTGGAACCGAGCAATG                         ATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAA
genomic: CCTTGCGCAATTTAGTGCAGATAATTCGTGGAACCGAGCAATGgtgagattta ... acatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatattgtgttcctgtttcttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT
                                        atttgac  putative branch site (score: 4)
                  tttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagcaataacttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttcttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -caataac
- - - - - - - - - - - - - - -acaagaa