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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagctaaaatttcaaatttgagcctgaagtattttcttcaaacatgaatgaaattattaaatttatgtacatttttaaaattattttttttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCAATTTACCTGCCGAAGAGGTGCCTCCAGAGCTTCCTGAGCCTGCACTAGG

Basic information

species Vitis vinifera
transcript Vv04s0008g01670.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g41740.1 (Oryza sativa), 3'ss of exon 2
ttagctaaaatttcaaatttgagcctgaagtattttcttcaaacatgaatgaaattattaaatttatgtacatttttaaaattat---tttttttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCAATTTACCTGCCGAAGAGGTGCCTCCAGAGCTTCCTGAGCCTGCACTAGG
    |||  |   | |   ||| |||||  | ||     |  | | |  |  || || || |||| |  |    |  | ||  ||   ||| | |  |  |||| ||||||||| | ||||||||||| ||||||| |||||| |||||||| ||||| || || ||||||||||| || ||||| || ||||| ||| | ||
-ctcctagtacacctatgctga-cctgatat-ttgagcactcataagcgtttaactaatatatttgtccagccatacataaccatgcgtttctctttctgcagAAAAGGAAAACTTGTGCCTTTATGGGTTTCCCAATGAGCATTGGGAAGTAAATTTGCCCGCAGAAGAGGTGCCACCTGAGCTCCCAGAGCCAGCATTGGG

upper sequence: Vv04s0008g01670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G11400.3 (Glycine max), 3'ss of exon 1
--------ttagc-taaaatttcaaatttgagcctgaagtattttcttcaaacatgaatgaaattattaaatttatgtacatttttaaaattattttttttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCAATTTACCTGCCGAAGAGGTGCCTCCAGAGCTTCCTGAGCCTGCACTAGG
         |||| |  ||| |    | |     |||| | |||| || | || | |   |  ||||| || ||||||    |||   || | |  |         |||| |||||||| || ||||||||||||||||| ||||||||||||||||||||| | || || || |||||||| || |||||||| ||||| ||| | ||
gtattgctatagcatttaatgttttttgtattgttgaaat-ttttgttgagactttagatattttattcaacttatgtgagctttgtgaactgtgat--------gcagAGAAGGAAAATCTTTGCCTTTATGGATTTCCAAGTGAGCAGTGGGAAGTCAATCTGCCAGCTGAGGAGGTGCCCCCTGAGCTTCCAGAGCCAGCATTGGG

upper sequence: Vv04s0008g01670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ21827 (Selaginella moellendorffii), 3'ss of exon 2
------ttagctaaaatttcaaatttgagcctgaagtattttcttcaaacatgaatgaaattattaaatt-----tatgtacatttttaaa--attattttttttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCAATTTACCTGCCGAAGAGGTGCCTCCAGAGCTTCCTGAGCCTGCACTAGG
      | |  ||    |       |     |    | | || ||    |  | ||  | | |||||| |     |     | ||  |       | |||||| |     |||||||||||||||| ||||| ||||||||||||   |||   ||||| || ||||| || || ||||| || ||||| ||||| || ||||| || || ||
gtgcgctcatttagttctcagggccttgaatttttttctctttttttctctcggatagagtgattaaactctgcctgccgccgttcgtgcgtgggtgttttttgtgtgtgcagACAAGGAAAACCTGTGCCTGTATGGATTTCCCGACGAGAGCTGGGAGGTGAATTTCCCAGCGGAAGAAGTTCCTCCGGAGCTCCCGGAGCCGGCGCTCGG

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|71864525|gb|DT013580.1|DT013580
EST:     ATGTTGAAGAATTTTATCAGCAGTGCGATCCGG                         ACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCA
genomic: ATGTTGAAGAATTTTATCAGCAGTGCGATCCGGgttagggttt ... ttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCA
EST: gi|27578473|gb|CB001168.1|CB001168
EST:     ATGTTGAAGAATTTTATCAGCAGTGCGATCCGG                         ACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCA
genomic: ATGTTGAAGAATTTTATCAGCAGTGCGATCCGGgttagggttt ... ttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgaaattattaaatttatgtacatttttaaaattattttttttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCAATTTACCTGCCGAAGAGGTGCCTCCAGAGCTTCCTGAGCCTGCACTAGG
                                           ttttaac  putative branch site (score: 2)
                                    ttatttttttt  CT-rich tract
      aaattattaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagctaaaatttcaaatttgagcctgaagtattttcttcaaacatgaatgaaattattaaatttatgtacatttttaaaattattttttttaaccacagACAAGGAAAACCTATGCCTTTATGGATTTCCCAGTGAGCAGTGGGAAGTCAATTTACCTGCCGAAGAGGTGCCTCCAGAGCTTCCTGAGCCTGCACTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - -agcctga
- - - - - - - - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - -aatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtac