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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT

Basic information

species Vitis vinifera
transcript Vv18s0001g06290.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 1
-----------------------gttcgatccacgaaaaccaatttgcaattcatgatc---tccggccattcttcaatgtttcaaaaccctaatttg---atattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
                       | | ||||| | | |     |  | | || ||| |    |  |    || ||   ||  |       || ||| |      ||| |  |  ||||| |||||||| |||||||| |||||||| || |||||||||||||| ||||| || || |||||||| ||
gtaagacgctcctcgtcgccgttgctggatcccccagatgagctagggattttatggtagggttagatttttttttcgtgggt--ggcttctgattcgtgtggtttccgccttcgtttt-cagTTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 1
----------------gttcgatccacgaaaaccaatttgcaattcatgatc---tccggcca-ttcttcaatgtttcaaaacc----ctaattt----gatattctgtgtgtgttttg--cagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
                 | |  ||| ||    | |  | |   |    ||||   ||||||   || ||   |||  |          || ||||    |     |||    |||||||  |||||||| ||||| || |||||||| || |||||||||||||| ||||| || || |||||||| ||
gtacccatttctcctcctcccctccccgcgggcgacgtggtcgtct-cgatccggtccggctggttgtttcttgtagcgcggtttgatctgattttgtggtcgccctgatgatgttttgcgcagTTCAACATCGCCAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaatttgatatt-ctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
                                                                 || | |   ||                |  | || ||      |   | | ||| |      | |   || || |  || || |  || |||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| ||||| || | ||||||
gttctcttcttcccaaaccctagttttttatattgctgtcgtatcttctctctgctacgtcgttttttgttttgcgttcgttgccgaagtcgttttaatttcttattgtcgctta-tgtgtattcttcgttgcttcatttcgctttgcgccttctgcagTTCAACATCGCGAATCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCTGAAACT

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 1
gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
||| | |   |    |  ||     | ||     ||| |  | |||  |   | ||   |     ||  |    |  |    |||  |||||||||||| || |||||||| ||||| || || ||||||||||| ||||| || ||||||| ||| ||
gtttgttttcctctga--aaccctaatttttctctctgcttcgatttcttgctattgggattaattatgtacgcacacaacttgt--tttgcagTTCAACATTGCGAATCCCACCACTGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
---gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
     | |  |   |||| || | ||    ||  ||  || ||     |   || ||   | ||    ||  |    |  |    | |  |||||||||||| || |||||||| ||||| || || ||||||||||| ||||| || ||||||| ||| ||
gtttgttgtcctctgaaaccctacttttgctttctg--cttcgatttcttgccattgggactaa---ttatgtccgcacacaacttct--tttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgatccacgaaaaccaatttgca-attcatgatctccggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
      | |  ||   | || | | | |  |   |  |  |  | |  |  | | |         ||||  |  | |  ||| | |   || ||||||||  | |||||||| || || ||||||||||||||||| ||||| |||||||||||||||||
-----gtgcgtgacggcgaaatcgaatagactctacatttgctcgtattcgagtttcctttg---ctaacctttt-tcatgtttcttcgtttcagTTCAACGTTGCGAATCCAACTACTGGATGCCAGAAGAAGCTCGAGATCGACGATGACCAGAAACT

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S31_322V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaattt-------gatattctgtgtgtgttttgc--agTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
                            |||  | | |      |  ||||  |||  |   |      ||| |  |     |   |     | | |       ||    |||  ||  | ||||  || |||||||||| ||||| |||||||| |||||||||||| | ||||| || || |||   || ||
gtgtgctgtacgctccgcatattctctctcgtacaatgctgctgatgttgccgttccaggggtggaattattttggacgtgcttgcatttgcagtgttggagaggactaactgcttgcttcttgcgcagCTCAATATCGCTAATCCCACCACAGGGTGCCAGAAGAAGGTCGAGATCGATGACGACGCTAAGCT

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|110710093|gb|EE086127.1|EE086127
EST:     CGCCAGCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110731210|gb|EE109174.1|EE109174
EST:     CCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110369359|gb|EC933517.1|EC933517
EST:     TTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: TTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|29782562|gb|CB347995.2|CB347995
EST:     CTCATCTCTTTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGGCCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CTCATCTCTTTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110724727|gb|EE100810.1|EE100810
EST:     CCGCCAGCCTCCTCTCTGATCCAGGATGAAA                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CCGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110694354|gb|EE071389.1|EE071389
EST:     CTCATCTCTTTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CTCATCTCTTTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110701201|gb|EE078523.1|EE078523
EST:     CCTCCTCTCTGATCCAGGATGAAA                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|30124734|gb|CB910073.1|CB910073
EST:     CTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110422092|gb|EC988404.1|EC988404
EST:     TTCGCCAGAGCCGCCAGCCTCCTCTCTGACT-CTGGATGAAA                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: TTCGCCAGAGCCGCCAGCCTCCTCTCTGA-TCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|28962095|gb|CB341128.1|CB341128
EST:     CGCCAGCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCTTACCACAGGATGCCAGAAGAAGCTTGAGATTGA
genomic: CGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCC-GACCACAGGATGCCAGAAGAAGCTTGAGATTGA
EST: gi|110729833|gb|EE106221.1|EE106221
EST:     CCTCCTCTCTGATCCAGGATGAAA                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|71858023|gb|DT007078.1|DT007078
EST:     CTCATCTCTTTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: CTCATCTCTTTCGCCAGAGCCGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
EST: gi|110698432|gb|EE075922.1|EE075922
EST:     AGCCGCCTTCCTCCTCTCTGATCCAGGATGAAG                         TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC
genomic: AGCCGCCAGCCTCCTCTCTGATCCAGGATGAAGgttcgatcca ... tgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT
                          taatttgatattct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgatccacgaaaaccaatttgcaattcatgatctccggccattcttcaatgtttcaaaaccctaatttgatattctgtgtgtgttttgcagTTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC