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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacgagttagaaatggcttaggcgctttgctctttagatgccagtacaaactgtttaataattgcatatttcattttgatttttggccttgttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTTTGGGAAAGACTTAAAAGAG

Basic information

species Vitis vinifera
transcript Vv13s0067g02950.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g02950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G22160.1 (Glycine max), 3'ss of exon 3
tacgagttagaaatggcttaggcgctttgctctttagatgccagtaca------aactgtttaataattgca---tatttcattttgatttttg---gccttgttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTTTGGGAAAGACTTAAAAGAG
           |||   ||       ||||   | | || | ||| |        | | |||| ||    ||     |||||||   ||| |     |||   || ||||||||| ||||||||||||||||| |||||||| || || ||  ||||||| |||   || ||||| || |||
-----------aataatttcaatctgttgcctctcaaat-ctagtgctccctttgattttttagtagacccaagacttttcattacaattgtataacgccgctttgtttcagATACCCTTATGATGAAGCTGCTACAGTGGCAATTTCTACCATCAAAGAATTTCCAAATGACTTTAAGGAG
















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|351034809|gb|FQ458166.1|FQ458166
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|71876452|gb|DT025507.1|DT025507
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|351014566|gb|FQ437568.1|FQ437568
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|349812975|gb|FQ411215.1|FQ411215
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|34550530|gb|CF518748.1|CF518748
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|110690444|gb|EE067550.1|EE067550
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|351014429|gb|FQ437431.1|FQ437431
EST:     AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
EST: gi|349815351|gb|FQ400506.1|FQ400506
EST:     AATAACGTTCAGTATATCGCCTTTCCTGTCATATCTGGTGGTGTTTTTGG                         ATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT
genomic: AATAACGTTCAGTATATCGCCTTTCCTGCCATATCTTGTGGTGTTTTTGGgtgagttgat ... gttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaactgtttaataattgcatatttcattttgatttttggccttgttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTTTGGGAAAGACTTAAAAGAG
                            ttttgat  putative branch site (score: 4)
                                         ccttgttctttc  putative PPT
        tttaataattgcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacgagttagaaatggcttaggcgctttgctctttagatgccagtacaaactgtttaataattgcatatttcattttgatttttggccttgttctttcagATATCCTTATGATGAAGCTGCCACAGTGGCTATATCCACTGTCAAAGAGTTTGGGAAAGACTTAAAAGAG

- - - - - -aatggct
- - - - - - - - - - - - - - - - - - gatgcca
- - - - - - - - - - - - - - - - - - - - - - tacaaac