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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaacaaacgcagtcatgagggaaaaactggatatcatttggtacttgtttttccacaatgcctaacttctcaaaaaaatacaatggtgatttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATAAAGATTGCTGTAAACACTGCTGCTAGGAGGGATGTTCTTGATATTGCTA

Basic information

species Vitis vinifera
transcript Vv00s0220g00110.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0220g00110.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 9
tgaaacaaacgcagtcatgagggaaaaactg--gatatcatttggtacttgtttttccacaatgcctaacttctcaaaaaaatacaatggtgatttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATAAAGATTGCTGTAAACACTGCTGCTAGGAGGGATGTTCTTGATATTGCTA
          | |  |   | | ||   ||   || |||||||| |  |||    |  |  |||| ||||     ||||| || | ||     ||   ||||||||  || |||||||||   || ||||| ||| | ||| ||||| | || ||| || ||||||||||||||||| |||||||  |||| ||||||||| 
----------gtaagctgcatgtaacttctatcgaaatcatttg-tggttgcaaatttattatgc-taaca----aaaaacatgcgatc----ttccctcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAGCTGATGCTTATTAAGGTTTCTGTAAACACTGCTGCTCGGAGGGAAATTCTAGATATTGCTG
















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|349818318|gb|FQ409093.1|FQ409093
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|352786516|gb|FQ479125.1|FQ479125
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351035256|gb|FQ458613.1|FQ458613
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351034594|gb|FQ457951.1|FQ457951
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351012893|gb|FQ430456.1|FQ430456
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351031526|gb|FQ459783.1|FQ459783
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351046895|gb|FQ454505.1|FQ454505
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351043332|gb|FQ451384.1|FQ451384
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351040114|gb|FQ425200.1|FQ425200
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351044506|gb|FQ443037.1|FQ443037
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|352795642|gb|FQ480230.1|FQ480230
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351017801|gb|FQ436154.1|FQ436154
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351032123|gb|FQ460380.1|FQ460380
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351054122|gb|FQ450204.1|FQ450204
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
EST: gi|351039410|gb|FQ461277.1|FQ461277
EST:     CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAG                         GTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA
genomic: CAATCAGTAAATTGGTTCAGCAACTTCAGAAGTTAATAGATCTCCATGAGgtgagagtta ... atttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttttccacaatgcctaacttctcaaaaaaatacaatggtgatttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATAAAGATTGCTGTAAACACTGCTGCTAGGAGGGATGTTCTTGATATTGCTA
                gcctaac  putative branch site (score: 2)
                                              tttgttc  putative PPT
                          tcaaaaaaatacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaacaaacgcagtcatgagggaaaaactggatatcatttggtacttgtttttccacaatgcctaacttctcaaaaaaatacaatggtgatttgttcagGTTCGCGATATTACCCACATGCCATTTGCAGAACGAGAGTTGATGTTGATAAAGATTGCTGTAAACACTGCTGCTAGGAGGGATGTTCTTGATATTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- aaacaaa
- - - - - gcagtca
- - - - - - - - - - -ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa