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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcattctgtgtagtccttattacatacttattccagcttacaagaattaagcatttttcctttgtatcattaacgtctttattttaactctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTTTGTTTTAAGAGCCTTTATGGTTTCCTAGCTCTTTTCTCAATTGGTGAAT

Basic information

species Vitis vinifera
transcript Vv00s0282g00040.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 10
tatcattctgtgtagtccttattacatacttattccagcttacaagaattaagcatttttcctttgtatcattaacgt-ctttatttta-------actctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTTTGTTTTAAGAGCCTTTATGGTTTCCTAGCTCTTTTCTCAATTGGTGAAT
         || ||    | | | |  | | ||   |  | | | ||| |     ||| |  |     | |||  | | ||| | || |         | | ||||||||||||||    ||||| ||| | || ||||||| ||| ||| ||||||||||||| |||||||||||||| ||| || |  | || ||| | || ||  
---tgcaaagtatatatataagtgcggagtaatg--aagtcaaaggaagt---tgtttcttgtgcaacttatttgcttgcttcagttcacaaaattgttttcttgcagCTTCTTTCTGGTGCAACTTTTCTTGGAGCAATATTTTGTTTTGGTGCCTTTTGTTTCAAGAGCCTTTATGGATTCATACCCTTCTTTTCAGTAGGAGAGC

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G164743_T01 (Zea mays), 3'ss of exon 12
tatcattctgtgtagtccttattacatacttattccagcttacaagaattaagcatttttcctttgtatcattaacgtctttattttaactctgt---tgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTTTGTTTTAAGAGCCTTTATGGTTTCCTAGCTCTTTTCTCAATTGGTGAAT
    |   |   ||   | | ||   ||    || ||       |    | |  || | |  | | |||  || | |  || ||   |  | | |   |||||||||||||    || |||||| | ||||||||||  |||||| |||| |||||||| |||||||||||||| ||| || |    ||  || |||| ||  
---gagcttaactaagtcattttgtgtagcgctttcaatcattgacccctcaaaatatattttgtttatttttcatggattcatgagacttttttccctgcagCTTCTTTCTGGTGCGACATTTGTAGGGGCAATATTCTGCTTTGGTGCTTTTTGTTTCAAGAGCCTTTATGGGTTCATACCCTCCTTTGCAGTTGGGGAGC

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G062024_T01 (Zea mays), 3'ss of exon 12
tatcattctgtgtagtccttattaca-tacttattccagcttacaagaattaagcatttttcctttgtatcattaacgtctttattttaactctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTTTGTTTTAAGAGCCTTTATGGTTTCCTAGCTCTTTTCTCAATTGGTGAAT
 | ||  |          | |||    |||   || ||       |     ||  | ||    | | |||  |    |  || ||   |  | | | ||||||||||||    || |||||| | ||||||||||  |||||| |||| |||||||| |||||||||||||| ||| || |    ||  || |||| ||  
aaccaaacaaccccaaagtcattttggtaccgctttcaatcgttgacccccaaaaaattgctatgtttatt-tccgtggattcatgagacttttctcgcagCTTCTTTCGGGTGCGACATTTGTAGGGGCAATATTCTGCTTTGGTGCTTTTTGTTTCAAGAGCCTTTATGGGTTCATACCCTCCTTTGCAGTTGGGGAGC

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|110376483|gb|EC941548.1|EC941548
EST:     GATTTAATGACATCTACAATCTCCAATGCTTTTAAG                         CTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTT
genomic: GATTTAATGACTTCTACAATCTCCAATGCTTTTAAGgtaggcactc ... tctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTT
EST: gi|71871367|gb|DT020422.1|DT020422
EST:     GAGGTTGTATTCTGGATTTAATGACATCTACAATCTCCAATGCTTTTAAG                         CTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTT
genomic: GAGGTTGTATTCTGGATTTAATGACTTCTACAATCTCCAATGCTTTTAAGgtaggcactc ... tctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattaagcatttttcctttgtatcattaacgtctttattttaactctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTTTGTTTTAAGAGCCTTTATGGTTTCCTAGCTCTTTTCTCAATTGGTGAAT
                                      ttttaac  putative branch site (score: 2)
                                            ctctgtt  CT-rich tract
                                tctttattttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcattctgtgtagtccttattacatacttattccagcttacaagaattaagcatttttcctttgtatcattaacgtctttattttaactctgttgcagCTTCTTTCAACAGCAACATTTTTCGGGGCAATATGTTGCTTTAGTGCCTTTTGTTTTAAGAGCCTTTATGGTTTCCTAGCTCTTTTCTCAATTGGTGAAT

- -cattctg
- - - - - - - - - - - - - - - - ttccagc
- - - - - - - - - - - - - - - - - - - - -acaagaa
- - - - - - - - - - - - - - - - - - - - - - - - ttaagca