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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcag

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaat------tgttgttgttactgcaaacatgggaacaaagatagttgtggagatat---tccacttttgggatgatactgaagcattctctttgcag
|  ||||  | ||||||||||| ||||||||||| ||||| ||||||||||| |||||| | || ||| ||||||| ||||| ||  ||||  | || ||||| |      ||       ||    |   |   | |||| | |  ||  | | || |   |    ||||  | ||||   |    ||||||| | |||
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTTGGAAAACTGGAAGAATGTCTTCAATTGTTAATCGAAAGgtattgccatttgccaagactatcctatttaatagtacaatgcttattcagaaaatgtattttttattttatggtgatcacgttatattctctatacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 11
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaat------tgttgttgttactgcaaacatgggaacaaagatagttgtggagatat---tccacttttgggatgatactgaagcattctctttgcag
|  ||||  | ||||||||||| ||||||||||| ||||| ||||||||||| |||||| | || ||| | ||||| || || ||| ||||  | || ||||| |      ||       ||    |   |   | |||| | |  ||  | | ||||   |    ||||  | ||||   |    ||||||| | |||
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAACTTGAAGAATGCCTTCAGTTGTTAATCGAAAGgtattgccatttgccaagactatcctatttaatagtacaatgcttattcagaaaatatattttttattttatggtgatcacgttatattctctatacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GRMZM2G443953_T01 (Zea mays), 5'ss of exon 21
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggag-atattccac-ttttgggatgatactgaagcattctctttgcag
| |||||| |  |||||||||  || |||||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||  ||||||| || |||||   | |  ||  | || |  |||     |  |   |||         |||   || || |  | ||| | |    | ||  || | |||
TGGCATCCATGTCTAAAGAACTAGGAAAGAACAATGTTGCTTTCCTTTGCTTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAGgtag--gcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattgtatgttgacaattggtcctttgctgtacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcag
| |||||  | || |||||||| || |||||||| ||||| ||||||||||| |||||| | || ||  ||||||||||||| ||  || |  | || |||||   |    ||     ||||   ||    || |  ||    |    || |||  ||||   | |  |        || |  | | |||
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgg----gcaagattgc---catacttaacctta---attttcttctttctagtttttgactc--tatcccttgtacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgtt----gttgt--tactgcaaacatgggaacaaagatagttgtggagatattccactt---ttgggatgata-ctgaagcattctctttgcag
|||||  ||||||||| || || ||||| ||||| ||||| |||||||| || || |||||||||||||| ||||| || || || |||||||| || |||||||  |     |||||  |  | |    |||  |  |  |||||    |||   |||  | |    ||    | |||  ||||| || |  |||||||
TTGCAATCCTTGCTAAGGAGCAAGGGAAAAACAATGTTGCATTCCTTTGCTTATTTATGTTGGGTAAATTAGAAGACTGCCTTCAACTGTTGGTAGAAAGgtaatcttctaaagttgtgctcttccctttatgacattactgatagggaaggattgattagaatgcagttacatttatagttgaagtatgccttttgcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgta-------attgttgt----tgttactgcaaacatgggaacaaagatagttgtggagatattccact----tttgg---gatgatactgaagcattctctttgcag
||||| | ||||||||||| || |||||||| || ||||| |||||||| || ||||||||||||||| | || || || || || || ||||| || |||||       | ||||||    | ||| |    ||||      | ||| ||     ||||   |  | |    |   |   ||||   ||||   || || || ||||
TTGCAACTCTTGCTAAAGAGCAAGGGAAGAATAATGTTGCATTCCTTTGCTTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 9
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgta-----------------------attgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgg--gatgatactgaagcattctctttgcag
||||| | ||||||||||| || |||||||| || ||||| |||||||| || ||||||||||||||| | || || || || || || ||||| || |||||                       |||  || | |||||| | | |  | ||    |   |  | || |  |||  | |   |   ||||   ||||   || || || ||||
TTGCAACTCTTGCTAAAGAGCAAGGGAAGAATAATGTTGCATTCCTTTGCTTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaatt------------gttgttgttactgcaaacat-gggaacaaagatagttgtggagatattc------cacttttgggatgatactgaagcattctctttgcag
|||||  |||||| || || || ||||| ||||| ||||| |||||||| || || |||||||||||||| ||||| || || || |||||||| || ||||||||            | |||| |   | |  ||||     | |  ||   |||   ||| |||       || |||     |    |||||| || |  |||||||
TTGCAATCCTTGCCAAGGAGCAAGGGAAAAACAATGTTGCATTCCTTTGCTTATTTATGTTGGGTAAATTAGAAGACTGCCTTCAACTGTTGGTAGAAAGgtaattttctaaagttgggctgttttccttcctgacattactgatagggaggattgattagaaatttagaatgcagtttacatttatagctgaagtatgccttttgcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatat-tccacttttgggatgatactgaagcattctctttgcag
|||||| ||||||||| ||||||||||||||||| |||||||| ||||| || || | | |||||| ||||||||| ||||||||| | |||||||| ||||| ||       ||||||   || |||       || |  |    | || | ||   | ||    | ||    |   ||| ||||  |||
TTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtattt-----cattactgttcacttggccgtttggaaaaat-caaatatgtgtcttttgttatctttatgacaagaaattatcttgacag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgg--gatgatactgaagcattctctttgcag
||||| | |||||||||||||| ||||||||||| || ||||| |||||  | |||||| |||||||| ||||||| ||| ||||| | |||||||| ||||||||       ||| |    || || ||     || | |     |  |  | ||| |||||   |   |     |  ||| | |   |||
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaatt-----cattagtagtcacttgagagtttggaaaatca---aatttatgcacctttggttaactgtgtgacaatattttttcctcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgta-attgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcag
| ||| | ||||| ||||| || || |||||||| || || || ||||| ||||||||||||||| || | ||||| || ||||| ||||||||||| ||||| ||||||  |  || | |  ||||| | | | | ||| |   | |  || |  || | |  | ||||| | |     | |  || |||
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtt--tactatttcttacatgtgga-acatatattcccgcaactaatt-acgtctatgctgatattaa-----tatggttacag

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|110728301|gb|EE103751.1|EE103751
EST:     TTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAG                         CAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAA
genomic: TTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttg ... ctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA