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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatctaaatattcacttacagcacacaatgtaccttgcttattttcaaggatgcccttggtaattttatttgtgtctctgaatttctacag

Basic information

species Vitis vinifera
transcript Vv10s0405g00020.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA15G12220.1 (Glycine max), 5'ss of exon 9
GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatctaaatattcacttacagcacacaatgtaccttgcttattttcaaggatgcccttggtaattttatttgtgtctctgaatttctacag
|||||||||||||| || ||||||||||| |||||||||||||||||| |  |    ||||||     | |||||||| |      ||  |  | | ||  ||||  ||  | ||  | | | ||||     |         
GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAGgtactataat--aatatt-----atagcacacatttggaagtgactggtcttaatcatgcgtttattgatgatttct-tgtcataacag--------

upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA09G01370.4 (Glycine max), 5'ss of exon 10
GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatctaaatattcacttacagcacacaatgtaccttgcttattttcaaggatgcccttggtaat--tttatttgtgtctctgaatttctacag
|||||||||||||| || ||||||||||| |||||||||||||||||| |     |||  |||   ||| |||||||| |      ||  |  | | ||  | ||  ||  | ||  ||||||    |  | |           
GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAGgtacta----taacaatt---ttatagcacacatttggaagtgactgctcttaatcaggcgtttattgatgatttattgtcataacag-----------

upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G01180.1 (Glycine max), 5'ss of exon 8
GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatctaaatattcacttacagcacacaatgtaccttgcttattttca-aggatgcccttggtaattttat-ttgtgtctctgaatttctacag
|||||||||||||| || ||||| ||||| ||||||||||||||||||||  |  || ||| |  |  |||    | |||||   |     | ||| | |    |   ||      ||||| |||  | | |    |  | |||
GAGTCAAGCAAGAGCATACAGATAGAAGCATTTCATGTTTTCAAGgtattatagttacataatggcccacattttaaaatgttattcttaaactttgacatcccgtgtttttcttctttatattgattttatcttgtcatgcag

upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT4G17270.1 (Arabidopsis thaliana), 5'ss of exon 9
GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtat------tgga-tctaaatattc--acttacagcacacaatgtaccttgcttattttcaaggatgcccttggtaatt---ttatttgtgtctctgaattt--ctacag-------------------------------------------------------------------
|| |||||||||| ||||||||| |||||||| ||||||||||||||||      || | ||||||||     | | |    || || || | | |  | ||     || | ||  |||| ||||   || || |  | | | ||| |   |  ||                                                                   
GAATCAAGCAAGACTATTCAGATAGAAGCTTTCCATGTTTTCAAGgtatatttcttgtactctaaatacatggagtaaatttacccagtgaaacataatcatcagtcag-acgct-ttggcaattggatttttcggattttttaatgtgattgtagtctgagttttgataataaagtcatgaaggggcaaccaaagttcactgatattgttgtttctgtacag

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|30129996|gb|CB915335.1|CB915335
EST:     GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG                         CTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
genomic: GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatc ... atttctacagCTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
EST: gi|30125722|gb|CB911061.1|CB911061
EST:     GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG                         CTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
genomic: GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatc ... atttctacagCTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
EST: gi|30136804|gb|CB922142.1|CB922142
EST:     GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG                         CTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
genomic: GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatc ... atttctacagCTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
EST: gi|110397538|gb|EC963286.1|EC963286
EST:     GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG                         CTGTTTGCTGCTAATCAAAACAAGCCCCCAGACATCGTGAGCATATTAGTT
genomic: GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatc ... atttctacagCTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
EST: gi|110381120|gb|EC946437.1|EC946437
EST:     GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG                         CTGTTTGCTGCTAATCAAAACAAGCCCCCAGACATCGTGAGCATATTAGTT
genomic: GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatc ... atttctacagCTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT
EST: gi|110724431|gb|EE100255.1|EE100255
EST:     GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG                         CTGTTTGCTGCTAATCAAAACAAGCCCCCAGACATCGTGAGCATATTAGTT
genomic: GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatc ... atttctacagCTGTTTGCTGCTAATCAAAACAAGCCCCCGGACATCGTGAGCATATTAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAGgtattggatctaaatattcacttacagcacacaatgtaccttgcttattttcaaggatgcccttggtaattttatttgtgtctctgaatttctacag

- -  AAGCAA
- - - AGCAAG
- - -  GCAAGA
- - - - - - - - - - - TTGAAG
- - - - - - - - - - -  TGAAGC