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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGTTGCAGCAAGGCTTGATGCGGAAGAAAGAAGAAACAGCACAAGATTGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgcttttgagctatgttctttgcttctatcatgctggctaacttgagaccagttggcatgcctccctggtgtatataattaatctttgttgtctctatcacatcag

Basic information

species Vitis vinifera
transcript Vv02s0025g02340.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02340.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os10g37630.1 (Oryza sativa), 5'ss of exon 2
TCTTGTTGCAGCAAGGCTTGATGCGGAAGAAAGAAGAAACAGCACAAGATTGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgcttttgagctatgttctttgcttctatcatgctggctaacttgagaccagttggcatgcctccctggtgtatataa-ttaatctttgttgtctctatcacatcag
 || ||||| || ||| ||||||| ||||| ||   |||||    | | ||| | ||||||||||||||||||||| | |  |||||||||||||| || ||| |||    |   |      | | || |  |||  |  ||     ||| ||  ||    | |||| | |   ||  ||||   || | |  |   ||||            
ACTCGTTGCTGCTAGGATTGATGCTGAAGAGAGGCTAAACAATCAACGCTTGCGTGAGGAACAAGATGCTGCTTATAGAGCTGCACTTGAAGCTGATCAGgtatgctaaactctggaggccatttctgttcttatattattgatgcgctttagtacaag-agtatgcatgctgtgta-atatgggttcaacgatagggtctg-----------

upper sequence: Vv02s0025g02340.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G31660.1 (Glycine max), 5'ss of exon 2
TCTTGTTGCAGCAAGGCTTGATGCGGAAGAAAGAAGAAACAGCACAAGATTGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgcttttgagctatgtt--ctttgcttctatcatgctggctaacttgagaccagt----tggcatgcctccctggtgtatataattaatctttgttgtctctatcacatcag--------------------------------------------------------
||||||||| || ||||||||||| |||||||||||||| |  |   | || |||||||| ||||||||||| ||  | |  |||||||||||||| |||||| |||  || |    |||| |   | ||||| | || |      |    ||    |       |||| || |    |    ||| | |  |  | |||  |   |  | |  ||||                                                        
TCTTGTTGCGGCTAGGCTTGATGCAGAAGAAAGAAGAAATAATATGCGCTTAAGGGAGGAGCAAGATGCTGCATACAGGGCTGCACTTGAAGCTGATCAAgtatgctttttgtagtgtatggttattctgcttgtttcctatcattttttgtggtctctactccatggcttgtccttttttcctatctcaacatcccttgcagaggcctttat-tcagaaagaactggcctgttactgttgctgtggattaatgttgtacgtatgcatgtccag

upper sequence: Vv02s0025g02340.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT4G10790.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTGTTGCAGCAAGGCTTGATGCGGAAGAAAGAAGAAACAGCACAAGATTGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgcttttgagctatgttctttgcttctatcatgctggcta-acttgagaccagttggcatgcctccctggtgtatataattaatctttgttgtctctatcacatcag
| | ||  | || ||| |||| ||||| |||||||||| ||      |  |||| |||||||||||||||||||| ||||  || |||||||| || |||||| | |  || ||  || |||     || | |       || | | |||| |      || |  | |   |    | | |    | |   |||||| |    || |      
TTTGGTAACTGCTAGGGTTGAGGCGGAGGAAAGAAGAACCAATCTGCGTCTGAGAGAGGAACAAGATGCTGCTTACCGTGCTGCTCTTGAAGCCGATCAAgtatgtt--ttctgttctttgtag---gcctgttcagaattgacaagacttta---tgattagtctactgtctaaatttgtggcgtca---tttgttctgctgattag-----

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|110402747|gb|EC963354.1|EC963354
EST:     AGGGAGGAAACAAGATGCTGCTTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAGGAACGGCTGGAAAGAGAAGCT
genomic: AGGGAGG-AACAAGATGCTGC-TTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
EST: gi|110363592|gb|EC927191.1|EC927191
EST:     GAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAGGAACGGCTGGAAAGAGAAGCT
genomic: GAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
EST: gi|110370570|gb|EC930038.1|EC930038
EST:     TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAGGAACGGCT
genomic: TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCT
EST: gi|30299679|gb|CB976473.1|CB976473
EST:     TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
genomic: TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
EST: gi|110684853|gb|EE062608.1|EE062608
EST:     TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
genomic: TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
EST: gi|161708570|gb|FC060429.1|FC060429
EST:     TTAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
genomic: TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
EST: gi|30299606|gb|CB976400.1|CB976400
EST:     TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAA                         GCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT
genomic: TGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgct ... atcacatcagGCTAGGGAACGCCAGAGGAAAGAAGAACAAGAACGGCTGGAAAGAGAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGTTGCAGCAAGGCTTGATGCGGAAGAAAGAAGAAACAGCACAAGATTGAGGGAGGAACAAGATGCTGCTTATCGTGAAGCACTTGAAGCTGACCAAgtaagctgcttttgagctatgttctttgcttctatcatgctggctaacttgagaccagttggcatgcctccctggtgtatataattaatctttgttgtctctatcacatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA