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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactgctctttcaaataaatcaaaatcaacttactcttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG

Basic information

species Vitis vinifera
transcript Vv17s0000g02140.t01
intron # 37
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: LOC_Os06g14740.1 (Oryza sativa), 3'ss of exon 39
gtcactgct--ctttcaaataaatcaaaatcaacttactcttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG
|| | | |    |||| |  ||||   |  ||   || |   || | |||||| |  | |   |   ||  |  ||     |   |   || |||||  | || |||||||||||||||||||| ||| || | ||||| ||||| |||||||| ||||||||||| ||  | | ||| |||||||||||| |||
gttatttcctattttccatcaaat---atccattctattggattatttttttatacttgt--gtaatattttattttatggtacatatttttcagGCCTTGGAATTCATTGATGAAACTGGTATCGATTCTCTAGCAGTATGTATTGGAAATGTTCATGGAAAATATCCCCCCAGTGGACCAAATCTCAGATTTG

upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: GLYMA07G11610.1 (Glycine max), 3'ss of exon 35
---gtcactgctctttcaaataaatcaaaatcaacttactcttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG
   |  |   ||| |    |  | |||||||    ||  ||| | ||  |  ||||    |  ||    | ||| |||    ||  | |||| |||||   | | ||||||||||| ||||| ||||||||||||||||| ||||| || || || |||||||| |||||||||| ||| |||||||| ||| |||
gttgctatctctcctctgcactactcaaaatt---ttcttctgtgcttgtgctaaa----ttcat----ttatgcttg---ttgcattaatttcagGCATCAAAATTCATTGATGAGACTGGCATAGATGCTTTGGCAGTGTGTATTGGTAACGTGCATGGAAAGTACCCTGCAAGTGGTCCAAATCTGAGATTTG

upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: AT1G18270.1 (Arabidopsis thaliana), 3'ss of exon 39
gtcactgct--ctttcaaataaatcaaaatcaacttactcttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattg-cagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG---
|||  || |   ||| |        |||  |||  |      |      ||||     ||  |    |  |   ||     | | ||| ||  |||||||  || || || ||   ||||||||||||||||||||| || ||||| ||||||||||||||||| |||||     | || ||||| ||||  ||||   
gtccttgttggttttaagccccgataaatccaatctctcacctaacaaatttatgttgctaaaccaaactacaatttattat-tatgagttttcagGCTCAGGAATTTATGGA---AACTGGTATAGATGCTTTGGCTGTGTGTATAGGAAATGTCCATGGAAAGTACCCCAAGTCCGGTCCAAACCTCAAGCTTGATT

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|349820359|gb|FQ403975.1|FQ403975
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|349824597|gb|FQ413264.1|FQ413264
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGG
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGG
EST: gi|71870716|gb|DT019771.1|DT019771
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|71890098|gb|DT039153.1|DT039153
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTAT
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTAT
EST: gi|349808649|gb|FQ405793.1|FQ405793
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|30125587|gb|CB910926.1|CB910926
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|349826605|gb|FQ418696.1|FQ418696
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|349824745|gb|FQ414603.1|FQ414603
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|30130704|gb|CB916043.1|CB916043
EST:     ATGACTTGACCGTTGAAGATTATGAAGCNAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACT
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACT
EST: gi|349820676|gb|FQ408505.1|FQ408505
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|349808888|gb|FQ406738.1|FQ406738
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
EST: gi|27582127|gb|CB004822.1|CB004822
EST:     ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAG                         GCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC
genomic: ATGACTTGACCGTTGAAGATTATGAAGCAAAGCTGACTGATGTTGATCAGgtcactgctc ... tgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG
     tctttttaaaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactgctctttcaaataaatcaaaatcaacttactcttttctctttttaaaaatctcgatgtcatcatggttggccctgtgtgaattgcagGCTCTAGAGTTCATTGATGAAACTGGTATAGATGCTTTGGCAGTTTGTATCGGAAATGTCCATGGAAAATACCCTGCAACTGGCCCAAATCTCAGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA