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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattttttattttattttttgggtgcagttcatcaatcatttaatttgtgatttctttcattttacttcacagggttcctttccttccttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCTTTTCTTCCCGCATTATATGCTTCATTTCAG

Basic information

species Vitis vinifera
transcript Vv06s0004g03700.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA15G04850.1 (Glycine max), 3'ss of exon 14
ttgattttttattttatt-ttttgggtgcagtt-catcaatcatttaatttgtgatttctttcattttacttcacagggttcctttccttccttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCTTTTCTTCCCGCATTATATGCTTCATTTCAG
   | |    |  ||||| || |   |  | ||   | |||||  | ||  |     | |   | | |   | | ||| |    ||  | |  ||||  ||||||||||||||||| || || |||||||||||||||| |||||| ||||| ||||| || |||||||||||||| ||||||
-aaagtaacaaagttattattctaattttaattgtgtaaatcaagttata-gcagcatttacgactctttgtaataggatgggctttatacactttccacagGTGCATAGAGCTTGCGCAGAGAGAGAAATTCTTGACAAGTTGGACCACCCCTTTCTACCTGCATTATATGCTTCCTTTCAG

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 13
ttgattttttattttatt-ttttgggtgcagtt-catcaatcatttaatttgtgatttctttcattttacttcacagggttcctttccttccttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCTTTTCTTCCCGCATTATATGCTTCATTTCAG
   | |    |  ||||| || |   |  | ||   | ||||   | ||  |  |  | |  || |     | |  || |  | ||  | |  ||||   |||||||||||||||| || || |||||||||||||||| |||||| ||||||||||| || |||||||||||||| || |||
-aaagtaacaaaattattattctaattttaattgtgtaaatcgagttata-gcaacatttaccactcgttgtaattggatggcctttatacactttccaaagGTGCATAGAGCTTGCGCAGAGAGAGAAATTCTTGACAAGTTGGACCACCCTTTTCTACCTGCATTATATGCTTCCTTCCAG

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 15
ttgattttttattttattttttgggtgcagttcatcaatcatttaatttgtgatttctttcattttacttcacagggttcctttcctt-----ccttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCTTTTCTTCCCGCATTATATGCTTCATTTCAG
  | ||| || | ||    ||| |||        | |||  || | ||    |||      |||||     |  ||||  ||||         |  |  || |||||||||||||||||  | || ||||| || || ||||||||||| |||||||||||||| |||||||||||||| ||||||
--gctttattttctttgccttttggtatttccttttaatttttcagtt---aattaaaacaattttgtcctagtgggtcacttttaacagtaactgtaactacagGTGCATAGAGCTTGCACAGAGAGAGAGATACTCGACATGTTGGACCACCCTTTTCTTCCTGCATTATATGCTTCCTTTCAG

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|30324849|gb|CD008111.1|CD008111
EST:     ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
EST: gi|32267450|gb|CD716413.1|CD716413
EST:     ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
EST: gi|30325883|gb|CD009145.1|CD009145
EST:     ACTTTGTCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
EST: gi|30325043|gb|CD008305.1|CD008305
EST:     ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG                         GTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT
genomic: ACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAGgtattcaaat ... ttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgatttctttcattttacttcacagggttcctttccttccttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCTTTTCTTCCCGCATTATATGCTTCATTTCAG
 atttaat  putative branch site (score: 4)
                                ttcctttccttccttt  putative PPT
       atttctttcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattttttattttattttttgggtgcagttcatcaatcatttaatttgtgatttctttcattttacttcacagggttcctttccttccttttctgcagGTGCATAGAGCTTGTGCTGAAAGAGAAATTCTTGACATGTTGGATCACCCTTTTCTTCCCGCATTATATGCTTCATTTCAG

- - - - - - - - - - ttgggtg
- - - - - - - - - - - - - - - -tcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc