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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctctttctctctctctctctctctcaatgtgccacttgtttggattccacttttacccaatttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG

Basic information

species Vitis vinifera
transcript Vv13s0073g00610.t01
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 26
-----gtctctctttctctctctctctctctctcaatgtgcc----acttgtttggattccacttttacccaatttttattttttg--cttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG
      | |   ||  || ||       |||||   ||||||    | ||  |||  ||| |   ||  | || |||| | || ||   | ||||||| |||||||||||||| || ||||||||||||||||||||||||||  | || | ||| || |||||| | ||  |||| ||||||
gtaaattattgtttgttccctacaggcttctctagttgtgcccataaatttgttgtgttctatgatttacaaagttttctgttctgatttcttcagAGGAGAGATGTCTATGGAGCCTGGGAGCAGTATCTTGGTTTGGAGCATGCTGATACTGCACCAAAAAGGGCCTACACAGCCAATCAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GRMZM2G014805_T02 (Zea mays), 3'ss of exon 11
gtctctctttctctctctctctctctctcaatgtgccacttgtttggattccacttttacccaat-ttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG
|  | |  ||  ||     |   |   |  ||   |  ||    |  | | || |  |||   ||  |||  |||||  | | ||||| |||||||| |||||||||||||| || || ||||| ||||||||| |||| |   |  | |||||||| ||  |||| ||||||
gcatgtgatttccttatcatacttaaatgcatac-cttctctcattcactacattcatacatgatgctttgctttttattatacagAGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACCGATACAACATCGAAAAGGTCTTACACAGCCAATCAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
gtctctctttctctctctctctctctctcaatgtgccacttgtttggattccacttttacccaat-ttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG
|    |  ||   ||    |   |   |  ||   |  ||  | |  | |    |  |||   ||  |||  |||||  | | ||| | |||||||| |||||||||||||| || || ||||| ||||||||| | || |   |  | ||| |||| ||  || | ||||||
gcaagtgatttcttcagaatgcttaaatgcatac-cttctcttgttcactttgttcatacatgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 27
gtctctctttctctctctctctctctctcaatgtgccacttgtttggattccacttttacccaatttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG
                               |||||  ||  |      |      ||||  || |||        | |||  |||   | ||||||||||||||||||||||| || || |||||||||||||| ||||  || || ||  | ||  ||   |||| ||||
-------------------------gtagtttgtgctcctaatgctttatgtgtgcttacgtaactttgg-----ggatttgtagAAGCGGGATGTCTATGGTGCTTGGGAGCACTACCTGGGTTTGGAGCACTCGGACACAGCACCAAAGCGTTCTCATCTTGCTAGTCAG

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|110710415|gb|EE086729.1|EE086729
EST:     GTCGCCCTGAGTATCTTCAGGACTCTGACATTGTCTCTAGTCGATTCCAG                         AGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCC
genomic: GTCGCCCTGAGTATCTTCAGGACTCTGACATTGTCTCTAGTCGATTCCAGgtctctcttt ... tgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCC
EST: gi|351033616|gb|FQ447775.1|FQ447775
EST:     GTCGCCCTGAGTATCTTCAGGACTCTGACATTGTCTCTAGTCGATTCCAG                         AGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCC
genomic: GTCGCCCTGAGTATCTTCAGGACTCTGACATTGTCTCTAGTCGATTCCAGgtctctcttt ... tgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgccacttgtttggattccacttttacccaatttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG
                                  tttttattttttgctt  CT-rich tract
                        ttttacccaattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctttctctctctctctctctctcaatgtgccacttgtttggattccacttttacccaatttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT