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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctaattttctgaaaataagatagattctatagccttttacattttggtttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC

Basic information

species Vitis vinifera
transcript Vv01s0010g02760.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 15
ttttctaattttctgaaaataagatagattctatagccttttacattttggtttctttttgtcacactt-ttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC
|||| |  | | | ||   |   || | |    |     | | | |||  | | || |   |   |||   | |   |||  |   |  ||| |    ||||||||| || |||||||||||||||||||| || |||||||||||||| |||||||||||  ||||||| || ||||| ||||| ||||| || ||||  
ttttgtgttatacagacccttctattgttatattgtggatattcgtttatgatactgtaaatgggactgactaagttataatttactgccttgtaa-acagTGAAGGAGCAGGTGGTGGTCATGCTCCAGACATTATCAAAGTATGTGGAGTGAAAAATGTGTTACCCTCTTCAACAAATCCAACTCGGCCATTTACTTTG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
ttttctaattttctgaaaataagatagattctatagccttttacattt-tggtttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC
| || |  | | ||    |      | |||     |   | |   ||  ||| || |   |||||   || | || ||| |          || ||  |||||||||||||||||| |||||||||||||| ||||||||||| ||||| || ||||||||  | ||||| || ||||| || || ||||| || ||||| 
tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcat-catgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 12
ttttctaattttctgaaaataagatagattctata-gccttttacattttggt-----ttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC
      |||       | | | |  | |  | ||  | ||||||  || | ||     || | |||| |  | | ||||||  | | |   | | |  ||| ||||||||||||| ||||||||||||||||||||||||||||||||||||||| |||| |||||||| |||||||| |||||||||||||| ||||| ||   |
-----caatcacaaatagaaatggaaaacacaatgcgacttttattttctagtctaagttgtatttggctgattcttgatgtttctat-attgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 14
ttttctaattttctgaaaataagatagattctatagccttttacattttggtttctttttgtcacacttttgatgcat-atgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC-----
    |        |  ||||   | | |   | | || ||||   || |||| |   ||    ||     |||| | | ||||   ||| || ||     | | |||||| ||||||||||||||||||||||| ||||||||||||||| |||||||||| || |||||||| ||||||||||| || ||||| |||  |     
---ccatcacaaatagaaatggaaaacacaatgtggc-ttttgttttctggtctaagttg--tacttggctgattcttgatgtttctatattgtttacttgagcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 13
ttttctaattttctgaaaa---taagatagattctatagccttttacattttggtttcttt-----ttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC
        |   ||||||    ||  ||   |||| |   || | | || |   || |  |     ||| |  | | ||||   | |  |   ||| || ||| |||||||||| ||||||||||| ||||||||||||||||| ||||||||||||| ||| ||||| ||||||||||| ||||| || ||||| ||||  ||    
-------ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgac-taaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 12
ttttctaattttctgaaaataagatagattctatagccttttacattttggtttctttttg--tcacacttttgatgca-----tatgtcggt---atctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC
 ||  | |  |||| |       ||  |      ||    || | |    | || | ||||   || | | |||| |       | |||  ||   ||| || ||  ||||||||||||||||||||| ||||| ||||||||||| | ||| ||||| ||||||||||| || || ||||| || |||||||||||||| |  ||    
gttcatcagcttctcacctcttcatgcacctctcagatgcttccttcactgcttatgtttgaagcaaaatattgaagtgctatttttgtttgttaaatcattctggacagTGAAGGTGCTGGTGGTGGACATGCACCAGATATCATTAGAGTTTGTGGAGTGAAAAATGTACTCCCGTCATCAACCAACCCAACACGGCCATATACGAAA

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|161720992|gb|FC070359.1|FC070359
EST:     GAACATACAATTGCTGCGTTTAAAGATAGAACTATTCATACTTACCACAG                         TGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGT
genomic: GAACATACAATTGCTGCGTTTAAAGATAGAACTATTCATACTTACCACAGgtacaagttg ... ttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC
                      ttttgat  putative branch site (score: 4)
                                        tatcttttt  putative PPT
      tttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctaattttctgaaaataagatagattctatagccttttacattttggtttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC

- - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatatg