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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatctatgttttgcgcatatataactctaggtttgagactcatttatgttggcttctagtttctttatttctgattactgtttcacttgtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGCTATGGCATTGCTTTTGCAGAGGGGAAATCCTCGTTTTGCTCAGCTTAGT

Basic information

species Vitis vinifera
transcript Vv15s0048g00240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G027043_T01 (Zea mays), 3'ss of exon 1
ttcatctatgttttgcgcatatataactctaggtttgagactcatttatgttggcttctag---tttctttatttctgattactgtttcacttgtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGCTATGGCATTGCTTTTGCAGAGGGGAAATCCTCGTTTTGCTCAGCTTAGT
             |||   ||| |||    |  ||  | | |||  | |  |  | | |     |  ||  |  ||||||| ||| |       | ||   ||||||| |||   ||| |||||| | ||| ||| | |||| ||  || |||| || ||||||||||| || || ||||||||||||||||||||||| | |
---cctggccccatgcatgtatctaaaaagattttacatattcaactgtcatttcatgtgaatatgactacacctctgatttctgatgtttcaatttgcctagGTACTATGGACGCATGGATGTTACTGTGGCATTTTCTGCATTCGTTATTGCCATAGCATTGCTTTTACAAAGAGGAAATCCTCGTTTTGCTCAGCTAACT

upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G053711_T03 (Zea mays), 3'ss of exon 1
ttcatctatgt-tttgcgcatat-ataactctaggtttgagactcatttatgttggctt--ctagtttctttatttctgattactgtttcacttgtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGCTATGGCATTGCTTTTGCAGAGGGGAAATCCTCGTTTTGCTCAGCTTAGT
   ||  |||| |||  |||| | | |  || || | | |   |||| ||  |     |  |||     ||  ||||||||   |  |  |  | | || | ||||||| |||   ||| |||||| | ||| | | | |||| ||  |  |||| || ||||||||||| || || ||||| ||||||||||||||||| | |
---atgcatgtatttaagcattttacagatccagctgtcat-ttcatgtaaataaatatgactaccgatttggtttctgatgtttcatctatctatttgcttagGTACTATGGACGCATGGATGTTACTGTGGCGTTTTCTGCATTCGTCATTGCAATAGCATTGCTTTTACAAAGAGGAAACCCTCGTTTTGCTCAGCTAACT

upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 2
ttcatctatgttttgcgcatatataactctaggtttgagactcatttatgttggcttctagtttctttatttctgatt-actgtttcacttgtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGCTATGGCATTGCTTTTGCAGAGGGGAAATCCTCGTTTTGCTCAGCTTAGT
      |  |||| ||   || |   ||||| ||   ||  |   || |  |   |   |  |   || |   ||| | | | | | |  | | |  | ||||||||||||||||||||| | |  ||||||||||| || ||| ||||||| || |||||| |  | || || |||   || |||||||||||||| |||
-----gtgagtttagc---taaaacgctctacgtcgaagcttgtcttgttatccatgtgatatgacttctccttgactgattttatgaaatatctttttagGTACTTTGGTAACATTGATATATTGGTGACATCTGCAGCATTTGTTGTTGCAATAGCATTGTTAGTACAAAGAGGATCCCCACGTTTTGCTCAGCTGAGT

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|110691999|gb|EE070741.1|EE070741
EST:     GTGTCACGAGTTTGCTCTGTTATCTGTACTGTCATGCCGTTACTTACACT                         GTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGC
genomic: GTGTCACGAGTTTGCTCTGTTATCTGTGCTGTCATGCCGTTACTTACACTgtaagattca ... gtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGC
EST: gi|161713032|gb|FC062454.1|FC062454
EST:     GTGTCACGAGTTTGCTCTGTTATCTGTACTGTCATGCCGTTACTTACACT                         GTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGC
genomic: GTGTCACGAGTTTGCTCTGTTATCTGTGCTGTCATGCCGTTACTTACACTgtaagattca ... gtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGC
EST: gi|110699872|gb|EE077264.1|EE077264
EST:     GTGTCACGAGTTTGCTCTGTTATCTGTGCTGTCATGCCGTTACTTACACT                         GTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGC
genomic: GTGTCACGAGTTTGCTCTGTTATCTGTGCTGTCATGCCGTTACTTACACTgtaagattca ... gtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGC
EST: gi|71863135|gb|DT012190.1|DT012190
EST:     GTGTCACGAGTTTGCTCTGTTATCTGTACTGTCATGCCGTTACTTACACT                         GTACTTTGGGAACATTGATGTTTCCGTGACATCTGCTGCCTTTT
genomic: GTGTCACGAGTTTGCTCTGTTATCTGTGCTGTCATGCCGTTACTTACACTgtaagattca ... gtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTT
EST: gi|71862966|gb|DT012021.1|DT012021
EST:     GTGTCACGAGTTTGCTCTGTTATCTGTACTGTCATGCCGTTACTTACACT                         GTACTTTGGTAACATTGA
genomic: GTGTCACGAGTTTGCTCTGTTATCTGTGCTGTCATGCCGTTACTTACACTgtaagattca ... gtatggtcagGTACTTTGGTAACATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgttggcttctagtttctttatttctgattactgtttcacttgtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGCTATGGCATTGCTTTTGCAGAGGGGAAATCCTCGTTTTGCTCAGCTTAGT
                         ttctgat  putative branch site (score: 3)
             tagtttctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatctatgttttgcgcatatataactctaggtttgagactcatttatgttggcttctagtttctttatttctgattactgtttcacttgtatggtcagGTACTTTGGTAACATTGATGTTTCCGTGACATCTGCTGCCTTTTTTGTTGCTATGGCATTGCTTTTGCAGAGGGGAAATCCTCGTTTTGCTCAGCTTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - gcgcata
- - - - - - - - - - - - - - - - - - - - - - - - tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttc