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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatcaatatcattagctattttttttttttttggctttttggctggtccagtatgacattatttggttactaataactgtttttaactgaaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCCTTTTCAATTGCTTTCAACCCTGCAGGAACTAA

Basic information

species Vitis vinifera
transcript Vv00s0181g00120.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0181g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G30960.1 (Glycine max), 3'ss of exon 4
caatcaatatcattagctattttttttttttttggctttttggctggtccagtatgacatt-atttggttacta--ataactgttt-ttaactgaaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCCTTTTCAATTGCTTTCAACCCTGCAGGAACTAA
     ||| | | |    |    |  | || | ||     |    | | || | ||   ||  |   | || |    |  |||    ||   ||||| |||||| | |||||||||||||| || ||||||||| |||||||||| ||  |||| |||||||||||||| || |||||||| |||||
----gaattttactgctaagaactaatattatcggtagcattaaagatacattgtggtttttgtactgctattgtggtttctgaccatttgatgaaacttgcagTTACGTTGCACATATCGGGCATATGATGCTATGGATGAAATTACAGCTGCTTTTTCAATTGCTTTTAATCCTGCAGGGACTAA
















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|351013150|gb|FQ424855.1|FQ424855
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|351039899|gb|FQ464937.1|FQ464937
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|351018924|gb|FQ426423.1|FQ426423
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|33404273|gb|CF209900.1|CF209900
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|351047461|gb|FQ454953.1|FQ454953
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|351028547|gb|FQ444828.1|FQ444828
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|351052700|gb|FQ453808.1|FQ453808
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|33404557|gb|CF210184.1|CF210184
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|352798434|gb|FQ480459.1|FQ480459
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|351024039|gb|FQ423462.1|FQ423462
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
EST: gi|349832306|gb|FQ420867.1|FQ420867
EST:     GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAG                         CTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC
genomic: GTACTACTCGGGATCATCCCATTCACCTTTGGGATGCTGCTTCTGGTGAGgtatagaact ... aaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtccagtatgacattatttggttactaataactgtttttaactgaaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCCTTTTCAATTGCTTTCAACCCTGCAGGAACTAA
                          taataactgtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatcaatatcattagctattttttttttttttggctttttggctggtccagtatgacattatttggttactaataactgtttttaactgaaaattgcagCTGCGTTGCACATATCGAGCTTATGATGCTGTGGATGAAATCACGACTGCCTTTTCAATTGCTTTCAACCCTGCAGGAACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
caatcaa
- - - - - - - - - - - - - - - - tggcttt
- - - - - - - - - - - - - - - - - - - - tggctgg
- - - - - - - - - - - - - - - - - - - - - - - - -cagtatg