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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTATGCTGTAAAATTACACTTGATATTTTCCGCGACCCTGTCATTGCTCCAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttgattttaactttgcatgctcaaatctgtagatttcccataatttcattggcacatttgtgttaatctccaacgttatgataatctag

Basic information

species Vitis vinifera
transcript Vv00s0642g00010.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0642g00010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G22210.2 (Glycine max), 5'ss of exon 7
CCTATGCTGTAAAATTACACTTGATATTTTCCGCGACCCTGTCATTGCTCCAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttgattttaactttgcatgctcaaatctgtagatttcccataatttcattggcacatttgtgttaatctccaacgttatgataatctag
  | ||||||| ||||||||| || |||||||  || ||||| ||  |||||||||| |||||||||||||||| |||| ||||||| |||||  ||||||| ||   ||||||  |  || ||   ||   ||||| || | |     | |||| ||       ||||  |   | |||| |  | |  |     
TTTGTGCTGTAGAATTACACTCGACATTTTCCATGATCCTGTAATCACTCCAAGTGGACTTACATATGAGAGAGCAGTGATTCTTGAGCATCTTCAGAAGgtaac--ctgatttgcatgtttcaccttc---tctgttgaatgctttccacttcaatgaagtcagtgtgcaataattcaacttcttaaacag----

upper sequence: Vv00s0642g00010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G09930.2 (Glycine max), 5'ss of exon 5
CCTATGCTGTAAAATTACACTTGATATTTTCCGCGACCCTGTCATTGCTCCAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttgattttaactttgcatgctcaaatctgtagatttcccataatttcattggcacatttgtgttaatctccaacgttatgataatctag
  | ||||||| ||| ||||| || ||||| |  || ||||| ||  |||||||||| ||||||||||||||||  ||| ||||||| |||||  ||||||| ||   ||||||  |  || |||  ||     || |  ||| |||    |||| ||       ||||  |   | |||| |  | |  |     
TTTGTGCTGTAGAATCACACTCGACATTTTTCATGATCCTGTTATCACTCCAAGTGGACTTACATATGAGAGAGCTGTGATTCTTGAACATCTTCAGAAGgtaac--ctgatttgcatgtttcatcttctttattgaatgttttccac---ttcaatgaagtcaatgtgcaataattcaacttcttaaacag----

upper sequence: Vv00s0642g00010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G07370.1 (Arabidopsis thaliana), 5'ss of exon 7
CCTATGCTGTAAAATTACACTTGATATTTTCCGCGACCCTGTCATTGCTCCAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttgattttaactttgcatgctcaaatctgtagatttcccataatttcattggcacatttgtgttaatctccaa-cgttatgataatctag---
  |||| || || || || ||||| |||||||| || ||||| ||| ||||||||||| |||||||||| |||| ||   | ||||| |||||  ||||||||   |    | | | |  |   | ||   | |  ||   |    | ||  |  |   | ||||  ||||||  |   | ||||   |  |  |     
TTTATGTTGCAATATAACTCTTGAGATTTTCCGAGATCCTGTAATTTCTCCAAGTGGGGTTACATATGAAAGAGCAGCAATCCTTGAACATCTCAAGAAGgtt---tgcattatcatcgctcttttcttgtagccttaatctctataaaaaatattc--ctcattcctgttaaggtttgatcgtttacaccacttgatag

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|110429905|gb|EC996419.1|EC996419
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|110394654|gb|EC959869.1|EC959869
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATTTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|30329949|gb|CD013211.1|CD013211
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|34361657|gb|CF403242.1|CF403242
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|349821463|gb|FQ411084.1|FQ411084
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGGAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|46918566|gb|CN547895.1|CN547895
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|110394861|gb|EC960232.1|EC960232
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|46909914|gb|CN545289.1|CN545289
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
EST: gi|77578487|gb|DV218036.1|DV218036
EST:     CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAG                         GTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA
genomic: CAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttg ... gataatctagGTGGGCAAATTTGATCCAATTACCCGAGAGCCACTTAGTCAATCTCAGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTATGCTGTAAAATTACACTTGATATTTTCCGCGACCCTGTCATTGCTCCAAGTGGGCTTACATATGAGAGAGAAGTGCTTCTTGACCATCTGGAGAAGgttacatttgattttaactttgcatgctcaaatctgtagatttcccataatttcattggcacatttgtgttaatctccaacgttatgataatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA