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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcttgcctatgaacttcttttttctttaattttttggaacttatcaacactatcatgtttctttatttgattgaattaatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC

Basic information

species Vitis vinifera
transcript Vv09s0002g07500.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g55180.1 (Oryza sativa), 3'ss of exon 6
aagcttgcctatgaacttctttt--ttctttaattttttggaacttatcaacactatcatgtttctttatttgattgaattaatttttctttgtat---aat-cagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC
      ||  |  |  ||    |  | ||  | ||  |   | |||  |     |  | |   | ||| | | || ||| ||| ||    |   ||   ||| |||  | || ||||  ||||||||||| ||||| ||||||||| |||| ||| | |||||||||||||||||| |
------gctcaatatttttcactaatgctgcagttgatgccatcttgccttttttgcccttaatatttgtatcatggaagtaaattcaagtcacatttcaatgcagGTTGCCACTTTTTGGTGAATTTACCTGCCAAAATGCTGTTTTGGCTGAGAGATTCATTGAAGCAGGTAGCCC

upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 6
aagcttgcctatgaacttcttttttctttaattttttggaacttatcaacactatcatgtttctttatttgattgaat-----taatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC
    |||||  |      |   || | |   |      | ||  |||||| ||| | | | |   ||| ||| |  |       |||  ||| ||    |  ||||   || || |  ||||||||||| || || ||||||||| |||| ||||||||||||||||||||||||||
--ctttgcccctctgacacagattgcat--gtgcagcaggaca-atcaaccctaccctatatgagtatatgactacacgctaacaatgcttcatttccaatgcagATGGCCACTCTTTGGTGAATTTACTTGTCAAAATGCTGTTTTGGCTGAGCGTTTCATTGAAGCAGGTAGCGC

upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G117531_T01 (Zea mays), 3'ss of exon 4
aagcttgcctatgaacttcttttttctttaattttttggaacttatcaacactatcatgtttctttatttgattgaat-----taatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC
    |||||  |      |   || | |   |      | ||  |||||| ||| | | | |   ||| ||| |  |       |||  ||| ||    |  ||||   || || |  ||||||||||| || || ||||||||| |||| |||||||||||||||||||       
--ctttgcccctctgacacagattgcat--gtgcagcaggaca-atcaaccctaccctatatgagtatatgactacacgctaacaatgcttcatttccaatgcagATGGCCACTCTTTGGTGAATTTACTTGTCAAAATGCTGTTTTGGCTGAGCGTTTCATTGAAGCAG-------

upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G03260.1 (Glycine max), 3'ss of exon 6
aagcttgcctatgaacttcttttttctt---taattttttggaacttatcaacactatcatgtttctttatttgattgaattaatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC
 |||||   |      | ||||| ||||    ||| | ||||   || | | |   ||  |  | || ||||  | |   || || |   ||  | |    ||||||||||| || |||||||||||| ||||||||||| |||| || ||||| || ||||||| ||||||| |
-agcttaatttaatgttgcttttgtcttatacaatatgttggctgtt-ttatcttgatttttatactatatt-aactactttgatgtcatttcttttttctagAATTCCTCTATATGGTGAATTTACAAGCCAGAATGCTATTATTGCTGAGCGGTTTATTGAAGGAGGTAGCCC

upper sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 6
--aagcttgcctatgaacttcttttttctttaattttttgg--aacttatcaacactatcatgtttctttatttgattgaattaatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC
   |  ||    |||  ||| | | || |  ||  | ||||     | |||   | | | ||  |   |||  |  ||  ||   ||||  ||| | |    ||||||||||| || |||||||||||  ||||||||||| |||| || ||||| || ||||||| ||||||| |
cttaatttaatgatg--cttttgtcttatacaacatgttggctgcttgatcttgattcttattctatattaactactttgatgccttttcttttcttt--ctagAATTCCTCTATATGGTGAATTTACCAGCCAGAATGCTATTATTGCTGAGCGGTTTATTGAAGGAGGTAGCCC

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|349830343|gb|FQ420603.1|FQ420603
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATCTACATGCCAGAATGCTATTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351040934|gb|FQ443710.1|FQ443710
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|32250010|gb|CD715829.1|CD715829
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|349832835|gb|FQ422957.1|FQ422957
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGCTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351056671|gb|FQ443298.1|FQ443298
EST:     AGTCCATTGACAGCTTCATCTCTGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351014571|gb|FQ437573.1|FQ437573
EST:     GTCCATTGACAGCTTCATCTCCGGTTCCAGGAACTGTT-CAGAAGTTAAG                         AATTCCTCTTTACGGGGAATTTACATG
genomic: GTCCATTGACAGCTTCATCTCCGGTTCCAGGA-CTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATG
EST: gi|351024626|gb|FQ433041.1|FQ433041
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         A-TTCCCTCTTTACGGTGAATTTACA
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCC-TCTTTACGGTGAATTTACA
EST: gi|352794161|gb|FQ479403.1|FQ479403
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351040019|gb|FQ425105.1|FQ425105
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAAAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351051549|gb|FQ450101.1|FQ450101
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTGAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351045276|gb|FQ451724.1|FQ451724
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTGAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|351054751|gb|FQ462781.1|FQ462781
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAG                         AATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
EST: gi|110712220|gb|EE089589.1|EE089589
EST:     AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCGGAAGT-AAG                         AATCCCTCTTTACAGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG
genomic: AGTCCATTGACAGCTTCATCTCCGGTTCCAGGACTGTTTCAGAAGTTAAGgtttggtatt ... gtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacactatcatgtttctttatttgattgaattaatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC
                              aattaat  putative branch site (score: 3)
                                    tttttctttgt  CT-rich tract
              tttctttatttgattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcttgcctatgaacttcttttttctttaattttttggaacttatcaacactatcatgtttctttatttgattgaattaatttttctttgtataatcagAATTCCTCTTTACGGTGAATTTACATGCCAGAATGCTGTTATGGCAGAGCGTTTCATTGAAGCAGGTAGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- -cttgcct
- - - - - - - - - - - - - - - - - - - - - - - caacact