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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaactaagttttatactttgttgagtattcttgatttggaatttgaatgtcttttccctgatttcacatgaatgtcttgtgtttggtttttgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG

Basic information

species Vitis vinifera
transcript Vv06s0004g06730.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G37350.2 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------gaactaagttttatactttgttgagtattcttgatttggaat-ttgaatgt-cttttccctgatttcacatgaatgtcttgtgtttggtttttgatttca-agTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG
                                                                   ||    ||| ||      ||    |   |  |||||  || || | | |  ||||  || || |   |  | ||  |  |  ||    ||  |||  | |||||||||||||||||||||||||  |||   || |||||  | ||||| ||  || |||| || |  |||||||| || |||||||||||
gtaattaattaatttgttgttacttttttgttataatatgaatctcacacactgctttgttatgcctacctcatttcatttggctttagacaacttaaatttgagatctttattatgttttttgcttatatggta-aagtgattcattcttcacattgaattgaacagTGGCCATGGAAGCTTTTCAGACAGCCCTTTTCTAAATAGCCTGGTGGGACACATCTTGCATTCCTCAATTCTTGTGCCATACCATGGATG
















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|352768954|gb|FQ468145.1|FQ468145
EST:     GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTG                         TGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
genomic: GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcactt ... tgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
EST: gi|352777477|gb|FQ474105.1|FQ474105
EST:     GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTG                         TGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATACTGGGGCA
genomic: GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcactt ... tgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
EST: gi|161712917|gb|FC062390.1|FC062390
EST:     GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTG                         TGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
genomic: GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcactt ... tgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
EST: gi|294966337|gb|GW837588.1|GW837588
EST:     GCTGCCCAGGGGACCATGTTCTGGGCATTGTTTGTTCTTGGACATGACTG                         TGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
genomic: GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcactt ... tgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
EST: gi|352773722|gb|FQ472504.1|FQ472504
EST:     GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTG                         TGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
genomic: GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcactt ... tgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
EST: gi|351019690|gb|FQ439507.1|FQ439507
EST:     GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTG                         TGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA
genomic: GCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcactt ... tgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtcttttccctgatttcacatgaatgtcttgtgtttggtttttgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG
                                          ttttgat  putative branch site (score: 4)
                                         ttttt  CT-rich tract
                                         tttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaactaagttttatactttgttgagtattcttgatttggaatttgaatgtcttttccctgatttcacatgaatgtcttgtgtttggtttttgatttcaagTGGCCATGGAAGCTTTTCAGACAATCCTAAGCTGAATAGTATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - gaatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg