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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatcttgatatgattctgttgcttttctttttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT

Basic information

species Vitis vinifera
transcript Vv18s0166g00300.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 11
gtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatct-tgatatgattctgttgcttttctt-tttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT
           |||  |           |||| ||  ||      || |  ||| |   | | ||||||| ||| || ||   |  | ||||  ||||  ||||||||   |  ||||| |||||||||||||| || || || |||||||| || || || |||||| |||||||||| || ||| | || || || |||||| ||||||| ||| 
----------gtttgttcttgttcttccattgtaaaactttaccattaccttctttgcca-atacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 8
gtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatcttgatatgattctgttgcttttctttttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT
||  ||    | |  ||  | |   ||| |    | | |    |||  || |  | ||  || |  |  ||  ||     | ||    | | ||  | ||   | |  ||  ||||| |||||||| |||||||||||||| ||||| || |||||||| |||||| |||||||||||||||| ||||| | ||||  |||| | ||||| ||||
gtgagctttgaatctctctctatctattttatacattgtg---tttcactcttcagatcttata--ttatagtttatcccgctt----tacattattgttgaaaatattctgcagAACAGTGAAGCCATGGTTTCAATTGACATGCCAGCTGGTCCATCTGAAGTTTTAGTCATTGCCGACAAGCATGCGATTCCTCGTCATGTAGCTGCTGATT

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatcttgatatgattctgttgcttttctttttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT
                      |    ||| |    || | |  |||  ||||    | |      |    |||  | |  | ||| ||    | ||||||   ||  |   ||||| || || || ||||| ||||| ||||||||||| ||||| |||||||| ||||| ||||| ||| ||||||||| ||| ||| | ||||| ||||| |
--------------------gtatagatatcgttcatcaattacttt--tgtcc---taacttgtttggagtctctagactactct-ttaacctgctttttcccttact--gcagAACAGCGAGGCAATGGTCTCAATCGATATGCCTGCTGGTCCTTCAGAAGTCCTAGTTATTGCTGACGAACATGCTAGTCCAGTTTACATTGCAGCAGACT

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|30251428|gb|CB969161.1|CB969161
EST:     TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA                         AATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
genomic: TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAAgtaggcacac ... tcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
EST: gi|71885572|gb|DT034627.1|DT034627
EST:     TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA                         AATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
genomic: TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAAgtaggcacac ... tcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
EST: gi|351054495|gb|FQ450579.1|FQ450579
EST:     TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA                         AATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
genomic: TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAAgtaggcacac ... tcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
EST: gi|71882273|gb|DT031328.1|DT031328
EST:     TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA                         AATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT
genomic: TTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAAgtaggcacac ... tcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacacatcttatcttgatatgattctgttgcttttctttttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT
           tcttgat  putative branch site (score: 4)
                      ttctgttgcttttctt  putative PPT
                               ttttctttttttattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatcttgatatgattctgttgcttttctttttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT