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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactgaatccaacggcctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG

Basic information

species Vitis vinifera
transcript Vv16s0050g01090.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 5
-------------------gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactg-aatccaacggcct-gatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG
                     |    |  | ||   || |   ||      |  | |  |  | || |   |||  || | ||  || |    |    | | || |   |||  | | ||| ||  || ||  |  ||   |||||||||||| || ||||||||||| ||||| ||||||||  |||| ||||| || |||
gtaattatatttttcattttcatatgtttagcaaagcaaattagagaaggaaggtgttatgcttttgtgtgtttgtttctgtttcttgtggaataggatctgaattatgatctcatgaccttgaatttttgtggtctgtattcagCTCCACCATTCGGACAAATTCAACGGGGTGCCATATGGCTTGTTTTTGGGACCAAAG

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G29790.1 (Glycine max), 3'ss of exon 5
gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactgaatccaacggc-ctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG
                    | | ||  |   |          | | || || ||| |||| || |  ||| |||| ||| |   ||||  ||   |   ||| | || |    | |  | |||||| ||||| || || ||||||||||| || |||||||||||||| ||||| || |||
-------------------tagaagaagccaaaaaaagggaaatttatttctgttcattttattttaatttattttcattgtt--ctgatacccgtgatactggtgttgt----ctttatgtcagCTTCACCATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G52570.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactgaatccaacggcctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG
                  | | || ||| || |       |   |||  | || | | ||   | |  || || || |||| |||   |||    |   | |||  |  | |  ||  | | |||| |||||| ||||||||||||| || || ||||||||||||||  | || || |||
-------------gtttta-ataccatcgttaaccaacgct---cttaacgttcttcattccatatagttattattgatttacaa---aattttgctaac-gattatg-gctttatctttttagCTACACCACACAGACAAATTCAAAGGTGTACCATATGGGCTGTTTCTTGGACCAAAG

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|110362018|gb|EC925524.1|EC925524
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTTCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|110387779|gb|EC952475.1|EC952475
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTTCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|34549741|gb|CF517973.1|CF517973
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|34544824|gb|CF513056.1|CF513056
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|110422537|gb|EC988863.1|EC988863
EST:     GGCCCATCGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|110388927|gb|EC953729.1|EC953729
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTTCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|110422253|gb|EC988569.1|EC988569
EST:     GGCCCATCGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|110362556|gb|EC926099.1|EC926099
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTTCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC
EST: gi|110391353|gb|EC956321.1|EC956321
EST:     GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAA                         CTCCACCACTCAGACAAATTCAATGGGGTTCCATATGGGCTGTTCTTGGGC
genomic: GGCCCATTGCGAACGTGCCCTATTTCAGACGCGTAGCTGCAGCACACCAAgtaagcatgc ... atggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttaattttcaactgaatccaacggcctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG
                                    ttctgat  putative branch site (score: 3)
     ttaattttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactgaatccaacggcctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT