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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttataagaagaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatcttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA

Basic information

species Vitis vinifera
transcript Vv05s0062g01250.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G082330_T03 (Zea mays), 3'ss of exon 8
atatt--tataagaagaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatcttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
 ||||   ||   |        |  |  || || |||||    | |   || |  | |       | |||   | |      |      | | ||    |||||||| || | ||||||| ||  ||||||||| ||||||||||| ||||| ||||| |||||  | |||||| | || || || ||||| |||
gtattggcattctatttgcagcagtttgctgatgttaatcaagtaagagttctagtgatcttatttgcac---cataaaaatctcagactgtattttggcagGTTGCATCGGCACTTCTTAGTGCTGCATTTGTGTATGACATCTTTTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGCGTCATGATTGCA

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 8
atatttataagaagaatgagaaatcac-ttatcttaatgttttgaatct--------tttgataactcatgctacacactcttgcctgacatttgt-tatct--tcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
 ||  |  | ||       |   | |  || |  |  | |||  |  ||        |   ||| ||  ||  |||   |||  |       || |  ||||  |  || |||||||  ||||||| ||||||||||||||||| || |||||||| ||||| |||||||| ||||| |||||| |  | |||||||||||  ||
gtacctgaatgagttccttgtgtttatattgtactgctatttccacactcatttagctccaatatctgttggaacat-ttctcacaatttgcttatgcatctgatatcatagGTTGCAACTGTACTCCTTTGTTGTGCATTTGTATACGACATCTTTTGGGTATTCATATCTCCAGTGATATTCCAGAAGAGTGTTATGATTACA

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G47600.2 (Glycine max), 3'ss of exon 8
-------------atatttataagaagaatgaga-aatcacttatct-----taatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatcttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
              | |||||    | ||| | | ||||| || |||     | |  || | |    | |  |||  ||      | | | |  | || ||| || |||      | |||||||  ||||||| ||||||||||| ||||| |||||||| || ||||| |||||||| ||||| || ||| | || ||||||||||| || 
gtacccaaatggattctttatgtctacaatcaaataatcatttttctcttactcactttgttatgtatctattaaaacagctctaataatttctcatg-catctgatata-----atagGTTGCAACTGTACTCCTTTGTTGTGCCTTTGTCTATGACATTTTTTGGGTATTCATATCTCCAGTGATTTTCCACGAGAGTGTTATGATTGCC

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 8
-----------------atatttataagaa-gaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgt-tatct--tcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
                  ||||| ||  |   ||| |  ||| | | ||  |  | ||     | || | ||   ||     | |||    | |       |  |  ||||  |   | |||||||  ||||||| ||||||||||| ||||| |||||||| || ||||| |||||||| ||||| || ||| | || ||||||||||| |||
gtacccaaatggattctttatttctacaatcaaataatcaattaatcattcttctcttaccctttttgttatgtatctattaaaacagctctactaatttctcatgcatctgatataatagGTTGCAACTGTACTCCTTTGTTGTGCTTTTGTCTATGACATTTTTTGGGTATTCATATCTCCAGTGATTTTCCATGAGAGTGTTATGATTGCA

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G44490.1 (Glycine max), 3'ss of exon 9
-------------atatttataagaagaatgagaaatcacttatcttaatgttttgaatct----tttgataactcatgctacacactcttgcctgacatttgttatcttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
              |  || |    | | |  |   | | ||  |||| |  |||   ||     | || |    |||    |||| | |       ||| || ||||     | |||||||  ||||||| || |||||||||||||| || |||||||| ||||| |||||||| || || |||||| |  | |||||||||||  ||
gtacctgaatgaattccttgtgtttatattatgctgttattt-ccttactcatttcgttccaatatctgttggaacatttctcacaatttgcttatgcatctgatatc-----atagGTTGCAACTGTACTCCTATGTTGTGCATTTGTATACGACATCTTTTGGGTATTCATATCTCCTGTGATATTCCAGAAGAGTGTTATGATTACA

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 9
atatttataagaagaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatcttcacac-agGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
                            ||| ||| | |  |      | |  | | | ||| |     ||||    ||    |  |  |||  || | |||||||  ||||||||||||| || |||||||| |||||||| ||||||||||||||||| ||| | |||||  | || ||||||||||| |  
---------------------------gtatttta-tctagtttgctgtgtagtgaattatgat-tgttctctgttatgcttataatggtctgtactccagGTTGCGACTGTACTTCTTTGCTGCGCATTTGTCTATGACATTTTCTGGGTCTTCATATCTCCATTGATATTTCACGAGAGTGTTATGATTGTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 9
atatttataagaagaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatctt-cacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
              |||      | |  ||| ||  |  |   | |||||||  | | | |  ||     |||        | | | | |||  |||  |||||||| |  | ||||| |||||||||||| | ||||||||||| ||||| |||||||||||| |||| |||||  | ||||| ||||| || 
-----------gtaaattttctgt-atgtattttcctactaaaattcttttgtgatccctttgtatgtgttct--------aatgggtgtctcacacttagGTTGCTACCATTCTTCTCTGTTGTGCATTTTTCTATGACATCTTTTGGGTATTCATATCACCACTAATCTTCAAGCAAAGTGTAATGATTGCG

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|110688633|gb|EE067409.1|EE067409
EST:     TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG                         GTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC
genomic: TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAGgtaatgaaat ... cttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC
EST: gi|294965259|gb|GW838946.1|GW838946
EST:     TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG                         GTTGCTTCTGTACTTCTTTGTNGTGCATTTGTTTATGACATCTTCCGGGTC
genomic: TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAGgtaatgaaat ... cttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC
EST: gi|110731688|gb|EE106318.1|EE106318
EST:     TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG                         GTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC
genomic: TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAGgtaatgaaat ... cttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC
EST: gi|110687402|gb|EE064779.1|EE064779
EST:     TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAG                         GTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC
genomic: TTAGTTTAATGATAACAGTTTTGCAGATAGCTCGATTGCCTAATATCAAGgtaatgaaat ... cttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgataactcatgctacacactcttgcctgacatttgttatcttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA
                                         ttatcttc  CT-rich tract
                                    atttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttataagaagaatgagaaatcacttatcttaatgttttgaatcttttgataactcatgctacacactcttgcctgacatttgttatcttcacacagGTTGCTTCTGTACTTCTTTGTTGTGCATTTGTTTATGACATCTTCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA

- - - - -agaagaa
- - - - - - - - - - aaatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcatgc