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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttttccaacttgattatgcaattaaattatgagtcatttgggcttttgaatgaggttaatatgaacttagatgtcccatactctttttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA

Basic information

species Vitis vinifera
transcript Vv04s0023g00380.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 5
atgtttttccaacttgattatgcaattaaattatgagtcatttgggcttttga-atgaggttaatat-gaacttagatgtcccat--actctttttgtgtgt-agTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA
 |||   |  || |     |||   ||  |||   | | ||||||     ||| |||   ||   || |  | |   || ||  |  | | | |||   ||  |||| | ||   ||| || ||||| |||||||| |||||||| |||| ||| ||  |||||| ||||||||| ||||||||||| |||
-tgtagctggaatt--gccatgt--ttgcatttgaaataatttggcacactgatatgtccttgccattgctcatgagtgacctgtcaaatttgtttacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTGACCCAAAGGGATCCCAGAAGAAGGAAATGGAAGAA
















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|110375514|gb|EC940507.1|EC940507
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|33405511|gb|CF211138.1|CF211138
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|30303671|gb|CB980465.1|CB980465
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|71867156|gb|DT016211.1|DT016211
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110386306|gb|EC950891.1|EC950891
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|34320010|gb|CF372764.1|CF372764
EST:     GATTGTGCCAAATNTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110403098|gb|EC964255.1|EC964255
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110398724|gb|EC965198.1|EC965198
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110393823|gb|EC959339.1|EC959339
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|30303609|gb|CB980403.1|CB980403
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|161715778|gb|FC066182.1|FC066182
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110369298|gb|EC933452.1|EC933452
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|161719466|gb|FC066414.1|FC066414
EST:     AAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: AAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|77584187|gb|DV221146.1|DV221146
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGA
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGA
EST: gi|110685575|gb|EE062425.1|EE062425
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110418308|gb|EC984450.1|EC984450
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|71866927|gb|DT015982.1|DT015982
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
EST: gi|110418385|gb|EC984534.1|EC984534
EST:     GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAG                         TTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG
genomic: GATTGTGCCAAATTTGATATCAAGGAAGCATACAAATAGTGCAGCTACAGgtatgtagtt ... ttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttgaatgaggttaatatgaacttagatgtcccatactctttttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA
            ggttaat  putative branch site (score: 4)
                                tcccatactcttttt  putative PPT
              ttaatatgaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttttccaacttgattatgcaattaaattatgagtcatttgggcttttgaatgaggttaatatgaacttagatgtcccatactctttttgtgtgtagTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - -tccaact
- - - - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccca