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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT

Basic information

species Vitis vinifera
transcript Vv15s0048g02700.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 4
gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT
|||    | ||| || |   ||  | |  || ||    || ||| |    ||    |||| || |||||   |      ||||| |    | ||||||   ||  ||||||||||||| ||||| ||    |||||||||||||| ||| ||||||||||||| ||||  | ||||||| ||||     |||| |
gtgtgtctgtgatttca---tggttgt--actttgcactaggaaggccccga-atttgctaat-tgagaccttg-----ttttggtc--ctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT

upper sequence: Vv15s0048g02700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT
|||    |||  |||     | ||  |     ||  |   | || |     | |  |||| ||      ||       || ||| |    | ||||||   ||  | ||||||||||| ||||| ||    |||||||||||||| ||| | ||||||||||| ||||  ||||||||| ||||     |||| |
gtgtgtcttttgatt-----tcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgtt------ctcttggtc--ctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT

upper sequence: Vv15s0048g02700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G42150.1 (Glycine max), 3'ss of exon 4
--gtgcagttttgaattgaaattgactatccaccttattttaaga-atgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT
   |||||| ||||| | |   || ||| | |  |||  |||||   |    || || |   || | |      | | | | |||||||||  | ||||||||||||||||| ||  | |||||||| ||||| ||||||  ||||||||| ||||| ||||| ||||||  | |||| || ||| | ||||| |  |
gtatgcagtcttgaactaactatg-cta-ctaatttacattaagctgttgtcaggcgcacctttttatt----cccactccattttgtttatat-cagGATCCTCAAAATCCTAGTAGGAATCGTGGGTTTGCGTTTGTTTTGTATTACAATAATGCATGTGCTGATTATTCGCGGCAAAAGATGGCAAGTTCTAGCT

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|351029583|gb|FQ427423.1|FQ427423
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|349833092|gb|FQ416470.1|FQ416470
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|351033373|gb|FQ446605.1|FQ446605
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|349833094|gb|FQ416472.1|FQ416472
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|351020125|gb|FQ445732.1|FQ445732
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGTTTTTGCTTTTGTTGAGTA
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTA
EST: gi|110381778|gb|EC935359.1|EC935359
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|351014469|gb|FQ437471.1|FQ437471
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|349829473|gb|FQ420005.1|FQ420005
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|351015298|gb|FQ445582.1|FQ445582
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCC
EST: gi|351044546|gb|FQ443077.1|FQ443077
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|351041038|gb|FQ443814.1|FQ443814
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTAC
EST: gi|351019214|gb|FQ429374.1|FQ429374
EST:     AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAG                         GATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGC
genomic: AAGTCATTGAGGATATTGGTCCTGGTGCTGAGAACATTGAACTTATAAAGgtgcagtttt ... ttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT
                                     ccttttgttt  CT-rich tract
                                       ttttgtttaattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagttttgaattgaaattgactatccaccttattttaagaatgaatagacgaatgcttatgtgagagtctaatgccttttgtttaattacagGATCCTCAAAATCCAAGCCGTAATCGTGGTTTTGCTTTTGTTGAGTATTACAACAATGCTTGTGCAGATTATGGGAGGCAGAAAATGTCTAGTTCAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT