Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcttcattccttttatcctgtatcaattgggttgtgtgctccactcttggtgctaaatctcttgttttgcatgattatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC

Basic information

species Vitis vinifera
transcript Vv14s0083g00950.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g00950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G37720.1 (Glycine max), 3'ss of exon 4
aatcttcattccttttatcctgtatcaattgggttgtgtgctccactcttggtgctaaatctcttgtt---ttgcatgattatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC
  |  | | | |  || |     |  || |   ||  || |  |   ||||      | |  | ||||   |   |  |||| |   |       |  |||||||| ||||| |||||||| ||||||||| | || ||||| |||||||||||||||||||| ||||||||||| ||||| || || || || |||||||| 
--ttcttagtacaattgtagccaaaaaaatatatta-gtacaacgtccttgcattatattgccctgtttgttcctaaaattaatgattttctccatcatgcagGCGTAGGCTCTCAACTGTTTTGGTGCGACTAAAATTTGCTGAGCACTTGAAAGAAGCTGTCACGTACATTGAACAAGGGCATATACGAGTTGGTCCAGAG

upper sequence: Vv14s0083g00950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G30110.2 (Glycine max), 3'ss of exon 4
aatcttcattccttttatcctgtatcaat---tgggttgtgtgctccac-tcttggtgctaaat----ctcttgttttgcatgattatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC
        ||| |  ||   ||||  |||   |   || | ||  | || |||| |   || |     || ||  ||   |  |||| |   |       |   ||||||| ||||| |||||||| |||||| || | || ||||| |||||||||||||||||||| ||||||||||||||||| || || || || |||||||| 
--------ttcttagtaaattgtaaaaataaataaattctttgtgcaacgtctttgcattatactgccctgtttgttcctaaaattaatgattttctccatcgggcagGCGTAGGCTCTCAACTGTTTTGGTGAGACTAAAATTTGCTGAGCACTTGAAAGAAGCTGTCACGTACATTGAGCAAGGGCATATACGAGTTGGTCCAGAG

upper sequence: Vv14s0083g00950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G06220.1 (Glycine max), 3'ss of exon 3
---aatcttcattccttttatcctgtatcaattgggttgtgtgctccac-tcttggtgctaaatctcttgttttgcatgattatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC
   ||||  | |||   | |   |   |     |   | | |||   |  |     || |   |        ||  |||||| |||  || | | | || ||||||  ||||| ||||| || ||||||||| | || ||||||||||||||||||||||| || || |||||||||||||| || || || || |||||||| 
tataatcaaccttctgctaaattttctttgtacgacctctttgcattatattgccctggtttgttcaaaaaatta-atgatttttt--tcgtctatcgt-gcagGCATAGGCTCTCAACAGTTTTGGTGCGACTAAAATTTGCAGAGCACTTGAAAGAAGCCGTCACATACATTGAGCAAGGGCATATACGAGTTGGTCCAGAG

upper sequence: Vv14s0083g00950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G15750.1 (Arabidopsis thaliana), 3'ss of exon 4
aatcttcattccttttatcctgtatcaattgggttgtgtgctccactcttggt-gctaaat-ctcttgttttgcatg------attatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC
     | |     | |          |  | ||  ||    |  || |||| | || ||||  |||  ||| |  ||      ||   ||  |  | | |  ||||||||| ||||| || |||||| |||| |   |||||||||||||||||   ||||||||||| || ||||| |||||||||||| | || || || ||||| 
----gtaagagtatatgcaagagcctatataggcagttacttaaacccttgatagccaaatgttctcatttcgtttgcctcatatcggttctttttttttatttgcagGCGTAGGCTATCTACTGTGCTGGTTCACCTGAAGTTTGCAGAGCACCACAAAGAAGCTGTGACATACATAGAGCAAGGACACGTTCGTGTAGGACCAGAA

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|26262363|gb|CA813426.1|CA813426
EST:     AGAAAAAGCTTGGCACTGTGTGATCGCTTAGCAGTGTCATCCTTTTGTAG                         GCGTAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAA
genomic: AGAAAAAGCTTGGCACTGTGTGATCGCTTAGCGGTGTCATCCTTTTGTAGgtaagtgaat ... gttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAA
EST: gi|351012591|gb|FQ430155.1|FQ430155
EST:     AGAAAAAGCTTGGCACTGTGTGATCGCTTAGCGGTGTCATCCTTTTGTAG                         GCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAA
genomic: AGAAAAAGCTTGGCACTGTGTGATCGCTTAGCGGTGTCATCCTTTTGTAGgtaagtgaat ... gttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttggtgctaaatctcttgttttgcatgattatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC
       tgctaaa  putative branch site (score: 2)
                           atgattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcttcattccttttatcctgtatcaattgggttgtgtgctccactcttggtgctaaatctcttgttttgcatgattatttgctcatatgttgttgcagGCGCAGGCTTTCAACTGTGTTGGTGCGATTGAAGTTTGCAGAGCACTTGAAAGAAGCTGTAACGTACATTGAGCAAGGACACATCCGGGTGGGTCCAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - -tcattcc
- - - - - - - - -tcctgta
- - - - - - - - - - - - - - - gggttgt
- - - - - - - - - - - - - - - - - - - -gctccac
- - - - - - - - - - - - - - - - - - - - - - - - -tggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcata