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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaaaattattgcattacagttatgagatggttgtaatgctaatatacaaagctcaccctgcttaactgccttaagtagttctcctgtttggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTATTATGGGAGTTGTCTTTGGATATTTTGTTGGTGTTTCATTTCCATCTGCT

Basic information

species Vitis vinifera
transcript Vv06s0004g02700.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------ttcaaaattattgcattacagttatgaga---tggttgta---atgctaatatacaaagctcaccctgcttaactgccttaagtagttctcctgtttggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTATTATGGGAGTTGTCTTTGGATATTTTGTTGGTGTTTCATTTCCATCTGCT---
                                                  || ||| ||     ||   |  ||| |     |  || ||      ||  |       |      || |   | |  || || |   | | || | |  |    |||  | ||   |||| |||| |||| ||| || || |||| |||||| ||||||||||| ||| |||||||| |||||||||| ||||| || ||||||     
gtaaggaaaaaattatttttagagttatgatgcctgcctttgttttgtattttaaattttaaatatcttaaatattaaggttttattttatgtgcactcgttctttgtgtatgttctacgagaatttctgaatttcatttactatctcttctttagTTCACTT---AAAAGATCAAATGATAGTACCCGGATTATCATCACAGCTATTATGGGAATTGCCTTTGGATTTTTTGTTGGTATTTCAATTTCATCTGTGCAT

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 2
---ttcaaaattattgcattacagttatgagatggttgtaatgctaatatacaaagctcaccctgcttaactgccttaagtagttctcctgtttggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTATTATGGGAGTTGTCTTTGGATATTTTGTTGGTGTTTCATTTCCATCTGCT---
       |||  |||   ||  ||      ||||  ||  ||  |  | ||        | | |  |   |    || |  | ||    |  ||  |   |  | |    || |||| |||| |||| ||| || || |||| |||||| ||||||||||| ||| |||||||| |||| ||||| ||||| || ||||||     
gtaagagaaaaaattattttgtagagtaatgatgcctgccattgttttgtatcttaaatatcttaatattccaattttaa-atttagtttactttctcttctttagTTCACTTAAAAGATCAAATGATAGTACCCGGATTATCATCACAGCTATTATGGGAATTGCCTTTGGATTTTTTATTGGTATTTCAATTTCATCTGTGCAT
















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|161717256|gb|FC067262.1|FC067262
EST:     TTTTGAATTGGGGTCATAGAATATACCAAGATGGGGACGTTACATCGCAG                         TGTAGTTCTNNNNNNNTCACATGACAGTGCCAGGCTTATAATCACAACTGT
genomic: TTTTGAATTGGGGTCATAGAATATACCAAGATGGGGACGTTACATCGCAGgtttaaatcc ... tggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTAT
EST: gi|110687082|gb|EE064179.1|EE064179
EST:     TTTTGAATTGGGGTCATAGAATATACCAAGATGGGGACGTTACATCGCAG                         TGGAGTTCTNNNNNNNTCACATGACAGTGCCAGGCTTATAATCACAACTGT
genomic: TTTTGAATTGGGGTCATAGAATATACCAAGATGGGGACGTTACATCGCAGgtttaaatcc ... tggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacaaagctcaccctgcttaactgccttaagtagttctcctgtttggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTATTATGGGAGTTGTCTTTGGATATTTTGTTGGTGTTTCATTTCCATCTGCT
                gcttaac  putative branch site (score: 3)
                                   ttctcctgttt  putative PPT
                           ttaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaaaattattgcattacagttatgagatggttgtaatgctaatatacaaagctcaccctgcttaactgccttaagtagttctcctgtttggttcgcagTGGAGTTCTAAAAAAATCACATGACAGTGCCAGGCTTATTATCACAACTATTATGGGAGTTGTCTTTGGATATTTTGTTGGTGTTTCATTTCCATCTGCT

- -aaaatta
- - - - - - - - - - - - - - - - - gtaatgc
- - - - - - - - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgcct