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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGCCACAGGAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagcgcaaaatgagctctatttaggtactagggaatgatgtccttaaactgaaagaaatggaatggttatgacattctgttgcag

Basic information

species Vitis vinifera
transcript Vv18s0001g12560.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G75220.1 (Arabidopsis thaliana), 5'ss of exon 12
-------------------------------------GTTATTGCCACAGGAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgag--ttagcgcaaaa---tgagctctatttaggtac----tagggaatgatgtcct-taaactgaaagaaatggaatggttatg-acattctgttgcag
                                     ||  | || || | |||  | || |||||| |||||||||| || ||||||||||| |||| ||||||  ||| | ||  |   | |  ||| |     | |    ||  ||| ||| |     | |   ||    |   ||||   ||| | | | | || |||
GAGTAACGCAGCAACATTTGGGGTCGGGGCTATTCAGGTAGTAGCGACTGCAATATCCACTTGGTTGGTGGACAAAGCAGGTCGTCGGCTTCTGCTTACTgtgagtattaactcattactttcatatctttccgacttccctctacagaaagatttaagacatatccaagattaactaatgcaaatggaaaatattttccag
















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|349811010|gb|FQ405998.1|FQ405998
EST:     GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|110384138|gb|EC948555.1|EC948555
EST:     GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|28968713|gb|CB347746.1|CB347746
EST:     CATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCCCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: CATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|33404093|gb|CF209720.1|CF209720
EST:     GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|110382391|gb|EC939356.1|EC939356
EST:     GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|33404176|gb|CF209803.1|CF209803
EST:     ATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: ATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|351014223|gb|FQ434812.1|FQ434812
EST:     GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|33402192|gb|CF207819.1|CF207819
EST:     GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: GAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
EST: gi|33402179|gb|CF207806.1|CF207806
EST:     AATTACTACATGGTTGCTGGACAAAGCTGGACGTC-GCNTTCTACTTATT                         ATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC
genomic: AATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGC-TTCTACTTATTgtgagttagc ... tctgttgcagATCTCCTCCTCTGTAATGACCATTAGCCTCCTAGTAGTTGCAGTGTCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGCCACAGGAATTACTACATGGTTGCTGGACAAAGCTGGACGTCGGCTTCTACTTATTgtgagttagcgcaaaatgagctctatttaggtactagggaatgatgtccttaaactgaaagaaatggaatggttatgacattctgttgcag

- - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - -  GCTGGA