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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatttttctgaatgcttctgctttcctttttcgatgtaaggatcctagtgagaaagaaataataacctgtccaattcaccaccataaaacccaag...

Basic information

species Vitis vinifera
transcript Vv08s0058g01360.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 10
TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatttttctgaatgct---tctgctttcctttttcgatgt-aaggatcctagtgagaaagaaataata-acctgtccaattcaccaccataaaacccaag
||| | ||    || || ||||||||||| || |||||||| ||||||||| | |||||||||   ||  | || |||   || |||||  | || ||||||  ||   |  | |  |        || |   |||| |  || | ||  |  | | |      | | | ||| || | | |  |    |   ||  |       
TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgcatgttgctctttcttcatatcaaacagtccactagttgtgcattcatatacttttgcggtctgtc-tgatctattt----

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA03G00510.1 (Glycine max), 5'ss of exon 10
TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatt-----tttctgaatgcttctgctttcctttttcgatgtaaggatcctagtgagaaagaa-ataataacctgtccaattcaccaccataaaacccaag
||| | || ||||||||| ||||||| |||||||||||||||||||| |||   || ||||    ||| || |||   |||||| |||||   |||||  |||||  ||     ||| ||||   ||||  ||  ||||||  |||  |   |   ||   |    |    | || |   |    |  ||  |  ||||       
TGCCAGTGCCCAGAGTGCCAATGCAAAAATACCTGGGGAAGTTATGAATGCTCATGTAGTGATGGTTTGTTCTACGCACGAGAAAATGACATGTGTATTGgtgagggttattgttttttgaagttttctaatt--ctttttgtatgccactttttaagactgccttactgcattagcagattttgtgtact-cattaaagttt---

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA18G44580.1 (Glycine max), 5'ss of exon 10
-TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatttttctgaatgcttctg-ctttcctttttcgatgtaaggatcctagtgagaaagaaataataacctgtccaattcaccaccataaaacccaag-
 ||  | || ||||  ||||||||||| || |||||||||||||| |||||||  ||||   |   ||| || |||  ||||||| ||||| | ||| |  |||||    ||| | | |  ||||  ||||   ||| |  | | |  ||   | ||  |||   ||  |    |||  |||     |   ||| ||      
CTGTCAATGCCCAGGTTGCAAATGCAAAAACACCTGGGGAAGTTACGAGTGCAAATGCAAAAGTGGTTTGTTCTACTCGCGAGAAAATGACACGTGTTTTggtgagg--ctttataagtttttctatctttttctttactctttcaaaatggcattgctaaatggattgtt-tttgtataatcatttaaagtaatactagttt

upper sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 5'ss of exon 10
TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatttttctgaatgcttctgctttcctttttcgatgtaaggatcctagtgagaaagaaataataacctgtccaattcaccaccataaaacccaag
||| | || |||||||| ||||| || || || |||||||||||||| |||||||||||   |  |||  | |||||||| || || ||| | || ||| || |           |||   ||| | |||||  |  |    |    |  |   |||  |  ||| | |   | | |  || |      | ||     ||
TGCCAGTGCCCAGAGTGTAAATGTAAAAACACTTGGGGAAGTTATGAATGCAGCTGCAGCAACGGTTTGCTTTACATGCGTGAGCACGACACTTGCATAGgtaaaag-------aaatagatcttccttcctccta-gccccatacttaatttggagtcattaatcagactttctgcttttgaatctggtgaatgtgtag

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|27579549|gb|CB002244.1|CB002244
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGATGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|32246668|gb|CD712487.1|CD712487
EST:     AGTGGCAATTTATTGTACATGCGAGAACATGATGCCGGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: AGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|33405593|gb|CF211220.1|CF211220
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|29781753|gb|CB346482.2|CB346482
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGATGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|110709458|gb|EE084946.1|EE084946
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|28959761|gb|CB339881.1|CB339881
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGGTGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|33405675|gb|CF211302.1|CF211302
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|22014493|gb|BQ799527.1|BQ799527
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|46910453|gb|CN545828.1|CN545828
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAG                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|110702269|gb|EE080793.1|EE080793
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|110390350|gb|EC955254.1|EC955254
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGATGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|30255039|gb|CB971486.1|CB971486
EST:     CGGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGCCATCATTT
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|110404060|gb|EC970018.1|EC970018
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|71875647|gb|DT024702.1|DT024702
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGATGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|110390265|gb|EC955167.1|EC955167
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGATGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
EST: gi|110371604|gb|EC935716.1|EC935716
EST:     CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGATGCCTGTATAA                         GTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC
genomic: CAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtattt ... atatatgcagGTAAACATGTTAAAACAGAGGTTAGCTGGAGCTTTATTTGGGTCATCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatttttctgaatgcttctgctttcctttttcgatgtaaggatcctagtgagaaagaaataataacctgtccaattcaccaccataaaacccaag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cataaaa