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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttccctcgtttgtttggcggtgtcctaacaggacaaagattgttatttttggaaggtgtttgatctcgctgttttggcattgactttttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGA

Basic information

species Vitis vinifera
transcript Vv04s0008g01750.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 1
tttttccctcgtttgtttggcggtgtcctaacaggacaaagattgttatttttggaaggtgtttgatctcgctgttttggcattgactttttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGA
  | |  |||||     |  | || |  |       |   |    |   || || |   ||| | |||  ||     | || |   |   ||     ||||| ||||| ||||| || ||||||||||||||||||||| || ||||| | || || || |||||||| ||||| |||||||| ||  | || || || |
-gtatggctcgtacccgtctccgtcttttg------cgtggcgcatgggttctgta---tgtctcatcatgcgtcgcttgc-tcacccgcttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA

upper sequence: Vv04s0008g01750.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 3'ss of exon 1
tttttccctcgtttgtttggcggtgtcctaacaggacaaagattgttatttttggaaggtgtttgatctcgctgttt-tggcattgactttttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGA
                 ||   ||||    |  |  |   | |  || ||       ||| |  ||| |   || || |     ||  ||||  | | ||||| || || |||||||||||||| ||||||||||| ||| |  | ||| | || |||||||| ||||| ||||| ||||| |||||  | || ||||| |
----------------gtgtgtgtgtagccattgttccccgctcatttttgccaatgggt-tgggatttttttgcttattattctgttttttcatgagcagTTCGTAGCGGATGGAGTCTTCTTTGCGGAGCTGAACGAGCTTCTCACCCGGGAGCTTGCTGAAGATGGGTACTCTGGCGTGGAAGTGCGCGTCACTCCCA
















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|71866153|gb|DT015208.1|DT015208
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|30295730|gb|CB972524.1|CB972524
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|32247633|gb|CD713452.1|CD713452
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|32270022|gb|CD719181.1|CD719181
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|33401617|gb|CF207244.1|CF207244
EST:     TCAGTTTCTGC-AACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: TCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|110728527|gb|EE104173.1|EE104173
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|352773252|gb|FQ470839.1|FQ470839
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|110732469|gb|EE107785.1|EE107785
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|32269891|gb|CD719050.1|CD719050
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|110688348|gb|EE066796.1|EE066796
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|77578758|gb|DV218182.1|DV218182
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|27582088|gb|CB004783.1|CB004783
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|110709636|gb|EE085271.1|EE085271
EST:     CTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: CTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|32272105|gb|CD721264.1|CD721264
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|30253062|gb|CB970613.1|CB970613
EST:     GAAGCTCAGTTTCTGCAATCATGGCGACGCAGATGAGCAAGAGGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|161705478|gb|FC055320.1|FC055320
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|352782408|gb|FQ470311.1|FQ470311
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|30326710|gb|CD009972.1|CD009972
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
EST: gi|161706215|gb|FC054973.1|FC054973
EST:     GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAG                         TTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA
genomic: GAAGCTCAGTTTCTGCAAACATGGCGACGCAGATGAGCAAGAAGCGAAAGgtcagtaact ... ttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttttggaaggtgtttgatctcgctgttttggcattgactttttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGA
                                   cattgac  putative branch site (score: 3)
                                         ctttttttc  CT-rich tract
                                          tttttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttccctcgtttgtttggcggtgtcctaacaggacaaagattgttatttttggaaggtgtttgatctcgctgttttggcattgactttttttcaacagTTTGTGGCTGATGGAGTCTTCTTCGCGGAGCTGAATGAGGTGTTGACCAGAGAACTTGCTGAGGATGGATACTCGGGCGTCGAAGTTAGGGTTACTCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- -ttccctc
- - - - - - -tgtttgg
- - - - - - - - - - - - - cctaaca
- - - - - - - - - - - - - - - - -ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgac