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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagccaattagaagttgtcatatttctctttgtatatcataatttgatctatgataggataaatcttagttctccatttcttgttctttgacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTTCAATCTGCTCCATACTACAACATGCCTGCCCAAACCCCTCATGCTGCTT

Basic information

species Vitis vinifera
transcript Vv09s0002g01530.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G04100.1 (Glycine max), 3'ss of exon 9
taagccaattagaagttgtcatatt----tctctttgtatatcataatt-tgatctatgataggataaat-cttagttctccatttcttgttctttgacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTTCAATCTGCTCCATACTACAACATGCCTGCCCAAACCCCTCATGCTGCTT
    ||||  |||  |||||   |     || | ||||   |||| ||     ||| | | |  |  |||   || |||   ||||| |   ||   |  | ||||||||||||||| ||||| ||| | ||||| || ||||| ||||| ||  | |||||| |||||||||| |||||||| |  ||||| |||||||| ||||
---accaaccagattttgtcgcttcctaatcaccttgttcttcatgatcgctttcttttacaaaactaatatctaattccttatttcctcccct---aattcacagGCTGAGACATCAGAAATCTGGTTACAGAATCCAAGGGACCTTCCTGGCATGCAATCTACTCCATACTATAACATGCCAGGGCAAACACCTCATGCAGCTT

upper sequence: Vv09s0002g01530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G00810.2 (Glycine max), 3'ss of exon 10
--taagccaattagaagttgtcatatt-tctctttgtatatcataatttgatctatgatagga-taaatcttagttctccatttcttgttctttgacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTTCAATCTGCTCCATACTACAACATGCCTGCCCAAACCCCTCATGCTGCTT
  | ||  |||| |    |  |  ||   || ||| |  || ||   ||  ||||| | |  | |||     | || ||  ||  ||  ||    |  | ||||||||||||||| ||||||||| | ||||| || ||||| | ||| ||  | |||||| |||||||||| |||||||| |  ||||| |||||||| ||||
aatcagataatttgtttcttcctaatcacctttttcttcatgatcgctt--tctattacaaaactaagatccaattttc--ttatttactcccctaattcacagGCTGAGACATCAGAAATTTGGTTACAGAATCCAAGGGACCATCCTGGCATGCAATCTACTCCATACTATAACATGCCAGGGCAAACACCTCATGCGGCTT
















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|37185533|gb|CF604886.1|CF604886
EST:     CATCCCGACTCAAGTACAAAGATGGCAACATTTACGTTCCAAATCCACAG                         GCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAG
genomic: CATCCCGGCTCAAGTACAAAGATGGCAACATTTACGTTCCAAATCCACAGgtaaaatcac ... gacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAG
EST: gi|110369149|gb|EC933296.1|EC933296
EST:     CATCCCGGCTCAAGTACAAAGATGGCAACATTTACGTTCCAAATCCACAG                         GCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTT
genomic: CATCCCGGCTCAAGTACAAAGATGGCAACATTTACGTTCCAAATCCACAGgtaaaatcac ... gacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTT
EST: gi|110726654|gb|EE102626.1|EE102626
EST:     CATCCCGGCTCAAGTACAAAGATGGCAACATTTACGTTCCAAATCCACAG                         GCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTT
genomic: CATCCCGGCTCAAGTACAAAGATGGCAACATTTACGTTCCAAATCCACAGgtaaaatcac ... gacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctatgataggataaatcttagttctccatttcttgttctttgacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTTCAATCTGCTCCATACTACAACATGCCTGCCCAAACCCCTCATGCTGCTT
                                         ctttgac  putative branch site (score: 4)
                         ttctccatttcttgtt  CT-rich tract
              ataaatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagccaattagaagttgtcatatttctctttgtatatcataatttgatctatgataggataaatcttagttctccatttcttgttctttgacctaacagGCTGAGACATCGGAAATTTGGATCCAGAACCCGAGGGAGCTTCCGGGTCTTCAATCTGCTCCATACTACAACATGCCTGCCCAAACCCCTCATGCTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
-aagccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggataaa