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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattaatttattcccttaacactatttactctatgctctttcttcctgctctttgacgtaaatttctcccattttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA

Basic information

species Vitis vinifera
transcript Vv08s0032g00600.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 18
----------------gtactattaatttattcccttaacactatt-----tactctatgctctttcttcctgctctt-tgacgtaaatttctcccattttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA
                 || | |  |   || |  | || |  |||      | | ||     ||  | |     ||   |  || || |  |    || | ||| | ||||||||| ||||||||||||  | | || ||||||   || || || |||||| | |||||||||||||||||||||||  ||||||| ||||| 
gtatatattttcatatctattttgcaagcatcctttaaaaaaaattagtacaattttaaaaaattagtacaaagactcacgtggtgaagtcattttgttgtacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTACGGGAAAACCATCTGAAATCCTGACAAAATTGAATGAAATGGCTGGATTTGCTCCAAATGAAGAAATTGAG

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 14
gtactattaatttattcccttaacactat-ttactctatgctctttcttc-ctgctctttgac--gtaaatttctcccatt--ttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA
      |  |||||||   |||||||  | | | |||    | || |||| |   |   ||||   |||  ||||  || |  || ||| | ||| || || || || || |||   |  || |||||   ||| ||  | || |||||||||||||||||||||||||  ||  ||||||| ||||| 
-----gtacatttatttgattaacaccttatcattcttccttattccttcacaaatggctgacacataacattctttcactgattgcagTTTTGTGGGGAGGCTCTTCGTAAAGGCCTTGGGAAAACCCTCAGAAATCTTGACCAAACTAAATGAAATGGCTGGATTTGTGCCAAATGAAGAAATTGAG

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 18
--gtactattaatttattcccttaacactatttactctatgctctttcttc-------ctgctctttgacgtaa-atttctcccattttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA
   |  |  |  || || |  ||  || | |||    |   ||  || | |          |    |||| | | ||  ||    | || ||| | ||| ||||| ||||||||||||  |   || |||||    || ||  | |||||||| |||||||||||||||||| ||||  ||||||| ||||| 
gtatgtttcttgttaatccatttgtcaatctttctgttgaacttcttttacagatgactcacatggtgacatgacatcgctttgctattacagTTTTGTCGGTAGGCTTTTTGTGAAGGCTCTGGGAAAACCGTCTGAAATATTGACAAAACTGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAG

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 18
------------gtactattaatttat-tcccttaacactatttactctatgctctttcttcctgctctttgacgtaaatttctcccatttt-----ccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA
             | |||||  ||| | | | ||    |  | |  | ||| | || |     || | | |   |||| ||| |     ||      |||| |||| ||| || ||  | ||||| |||||  |||| || || || ||      |||||| |||||||||| ||| ||||||||||||||||| || |||
gtgagaaaaacacttctatttgtttgtcttcttttgtcccttgtgttttatccactatacgt-tgttttcttttgtaattttttttttcttgtgctaccagCTATGCTGGCAGGCTGATGGTGAAAAGTTCCAGTAAGCCTATGGATATAACTGGAAAACTGAATGAAATGGTTGGCTTTGCTCCTGATGAAGAAATAGAA

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|71859919|gb|DT008974.1|DT008974
EST:     GATATTCTGCTTTTCTTCAAGCTTTATGACCCTGAGAAAGAAGAGCTCCG                         ATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCT
genomic: GATATTCTGCTTTTCTTCAAGCTTTATGACCCTGAGAAAGAAGAGCTCCGgtactattaa ... cattttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactctatgctctttcttcctgctctttgacgtaaatttctcccattttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA
                          ctttgac  putative branch site (score: 4)
                                      tttctcccattttcc  putative PPT
                                  taaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattaatttattcccttaacactatttactctatgctctttcttcctgctctttgacgtaaatttctcccattttccagATATGTTGGTAGACTTTTTGTGAAGAGTTCTGGTAAACCAATAGAGATTCTAACAAAACTAAATGAAATGGCTGGATTTGCTCCTGATGAAGAGATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA