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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatgtcatattgtttcttgtaaaaattgttttcttggttgggttgtgcttgtctccttctcttcactaatttgcttttgttgttattgtttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTCCACAGTTGCACTTGGCATTTCTGCATCAACAGCTTCCATAATCCTGGGT

Basic information

species Vitis vinifera
transcript Vv12s0028g01250.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01250.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G35280.1 (Glycine max), 3'ss of exon 1
---------caaatgtcatattgtttcttgtaaaaattgttttcttggttgggttgtgcttgtctccttctcttcactaatttgcttttgttgttattgtttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTCCACAGTTGCACTTGGCATTTCTGCATCAACAGCTTCCATAATCCTGGGT
            |||  ||  | ||  ||| ||   || || | ||| |||   ||  |||    | || ||    || |||| ||||  ||||| ||  ||    |||||||||||||||||| ||||||  ||||||||| || ||||| |||||||||||||||||||| |||||| | ||||||||||||||  | || || |||
aatcttttctgcatggtatgcttttcattgcaag--tttttattttgtttga--tgc-cttactcctttttcactgcttatttactttgcttgtttttaatt----tagTGCTACAATGGCTATCTATGACGCTGTACAGCTTGTGAGGGCCGATGTTTCCACAGTTGCACTCGGCATTGCAGCATCAACAGCTTCTGTTATACTTGGT

upper sequence: Vv12s0028g01250.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G34710.1 (Glycine max), 3'ss of exon 1
--------caaatgtcatattgtttcttgtaaaaattgttttcttggttgggttgtgcttgtctccttctcttcactaatttgcttttgttgttattgtttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTCCACAGTTGCACTTGGCATTTCTGCATCAACAGCTTCCATAATCCTGGGT
           |||   |    ||| |||| | | ||  | |  || |||   ||   |     | || ||    ||||||| ||||   |||| ||  ||    |||||||||||||||||| |||||    |||||||| || ||||| |||||||||||||||||||| |||||| | ||||||||||||||  | ||||| |||
atattttctgcatggtgtgccttttattgtcagattt--tgttctgtttga--tgccttacatcctttttcactgctaatttactttgcatgtttttaatt----tagTGCTACAATGGCTATCTATGATGCCGTACAGCTTGTGAGGGCCGATGTTTCCACAGTTGCACTCGGCATTGCAGCATCAACAGCTTCTGTTATCCTTGGT
















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|32269174|gb|CD718333.1|CD718333
EST:     CCCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAG                         TGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
genomic: CCCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAGgtacaccaac ... tttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
EST: gi|30137048|gb|CB922386.1|CB922386
EST:     CCCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAG                         TGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
genomic: CCCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAGgtacaccaac ... tttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
EST: gi|110719754|gb|EE095158.1|EE095158
EST:     CCCACCAAGGACATCAAGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAG                         TGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
genomic: CCCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAGgtacaccaac ... tttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
EST: gi|110698253|gb|EE075581.1|EE075581
EST:     CTCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAG                         TGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC
genomic: CCCACCAAGGACATCAGGCTCTTCATCAACTCCCCTGGTGGCTCCCTCAGgtacaccaac ... tttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttgtctccttctcttcactaatttgcttttgttgttattgtttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTCCACAGTTGCACTTGGCATTTCTGCATCAACAGCTTCCATAATCCTGGGT
                    cactaat  putative branch site (score: 2)
                                       ttattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatgtcatattgtttcttgtaaaaattgttttcttggttgggttgtgcttgtctccttctcttcactaatttgcttttgttgttattgtttgtactagTGCTACAATGGCTATTTATGACATTGTACAGCTGGTTAGGGCAGATGTTTCCACAGTTGCACTTGGCATTTCTGCATCAACAGCTTCCATAATCCTGGGT

- - - - - - - - - - gtaaaaa
- - - - - - - - - - - - - - - - - - -ggttggg
- - - - - - - - - - - - - - - - - - - - - - - gtgcttg