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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgtttgacattttgtcatctagactagactgagtcattgcattctcttggatctttattgagtattaactttttcattttgcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT

Basic information

species Vitis vinifera
transcript Vv17s0000g09740.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g18860.1 (Oryza sativa), 3'ss of exon 4
tctctgtttgac-attttgtcatctagactagactgagtcattgcattctcttggatctttat-tgagtattaactt--tttcattttgcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT
   ||| | | | | | |    | ||    | | || | ||||||||  || || || | |   ||| ||||   ||  | | || |      |   | ||||||| || ||||||||||| ||||| || |||||||| ||||| || ||||| || ||||||||||| ||||| || |||||| | || || ||||| || |
---ctgataggccagtatcaagtttacttgaaattgtg-cattgcataatcctgcatgtatgcctgaatattttattagtctaatctctttcctccctctgcagGGAACTGCTGATGAAGTAGTTGATTGGTCTCATGGTAAGCAACTATGGGAGCTTTGCAAAGAGAAATATGAGCCTTTATGGCTCAAGGGAGGGAAGCACT

upper sequence: Vv17s0000g09740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G039214_T01 (Zea mays), 3'ss of exon 4
tctctgtttgacattttgtcatctagactagactgagtcattgcattctcttggatctttattgagtattaact--ttttcattttgcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT
| | | |     |  |||  |  |    | |  | | |   |  | ||| | | ||  |  |||| |  | |||  |  ||||    | |  ||   || |||| || ||||||||||| || || || |||||||| || || ||||||||||| |||||||| |||||||| ||||||||| | |  || || || || |
tttttttacattaacttga-acatttcttggtttaatttgctcaaatctat-gcatgctatttgattcattactggtgctcatagctcttgctgaaatgtagGGAACTGCTGATGAAGTGGTGGATTGGTCTCATGGTAAACAACTTTGGGAACTTTGCAAAGACAAGTATGAGCCCTTATGGCTCAGGGGAGGAAAGCACT

upper sequence: Vv17s0000g09740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G24760.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------tctctgtttg-acattttgtcatctagactagactgagtcatt-------gcattctcttggatctttattgagtattaactttttcatttt-gcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT
                                     |    |||   | | ||   ||  |   | |||     |||||       | || ||  |  |    |  | ||| ||| |||     |    || | | | | ||||||| ||||| ||||| || ||||||| ||||||||| ||||||||||||||||||||| ||||||| ||||||||  ||||| | ||||| || || ||||
gtaagtttccgtgatcaaagattattgattggaagaattgaagttaataaagttgaacagatttgcaagatccgttcattcttgtatgaatccttgtctaataatcctcagtgttagcttaaaggtgaaagcttttcgatttgcagGGAACAGCGGATGATGTGGTTGACTTCTCTCATGGGAAGCAGCTTTGGGAACTCTGCCAAGAGAAATATGAACCGCTATGGCTCAAAGGTGGAAACCATT

upper sequence: Vv17s0000g09740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ19908 (Selaginella moellendorffii), 3'ss of exon 4
tctctgtttgacattttgtcatctagactagactgagtc-attgcattctctt--ggatctttattgagtattaactttttcattttgcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT
            |  |  |    | ||   || |   || | | ||||| ||    ||  ||| ||     |    |  |||  ||||| | ||  |  |||||| ||  | ||||| ||||| || ||||| ||||| |||||||| ||||| |||||||||||||||                                  
----------gtaggtgatgggatggaagggattagttccactccattccctctgagagttttctttgtcctcttttgattctctttgcgtgtt--tcggcagGGAACCTCGGATGACGTTGTGGATTGCTCGCATGGAAAGCAGCTCTGGGACCTCTGCAAAGAGAAG----------------------------------

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|71888035|gb|DT037090.1|DT037090
EST:     AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCAT                         GGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
genomic: AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCATgtaagtatca ... tgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
EST: gi|110732441|gb|EE107729.1|EE107729
EST:     AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCAT                         GGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
genomic: AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCATgtaagtatca ... tgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
EST: gi|110711539|gb|EE088132.1|EE088132
EST:     AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCAT                         GGCACAGCTGATAAAGTTTGT-GACTGCTCTCATGGCAAGCAGCTTTGGGA
genomic: AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCATgtaagtatca ... tgttgtgcagGGCACAGCTGATGAAGTT-GTTGACTGCTCTCATGGCAAGCAGCTTTGGGA
EST: gi|110684904|gb|EE062715.1|EE062715
EST:     AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCAT                         GGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
genomic: AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCATgtaagtatca ... tgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
EST: gi|110701178|gb|EE078479.1|EE078479
EST:     AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCAT                         GGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA
genomic: AATATTGACAAAATCCCATTGGTGCAGTGCCCTGTACTAGTGATTCATgtaagtatca ... tgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcttggatctttattgagtattaactttttcattttgcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT
                     tattaac  putative branch site (score: 1)
            tttattgagtattaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctgtttgacattttgtcatctagactagactgagtcattgcattctcttggatctttattgagtattaactttttcattttgcatattgttgtgcagGGCACAGCTGATGAAGTTGTTGACTGCTCTCATGGCAAGCAGCTTTGGGAACTCTGCAAAGAGAAGTATGAACCCTTATGGTTAAAAGGGGGGAATCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- -ctgtttg
- - - - - - - - - - - - - - - - - - - - - gcattct