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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcctaatgggagtccctagatttttgttctttgagtttggagaattgatttgttcccttatttataatttcaaaaattattccttgtttaaagtaaatgtgcaacttattttggaatcataaaaattaagcacataattacatcgatttatctcatctaggttcttgcttttatcatgttatgtgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGTTCCAAAAGTTTTATTGCTAAG

Basic information

species Vitis vinifera
transcript Vv14s0036g00520.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G36590.2 (Glycine max), 3'ss of exon 4
gtatgattcctaatgggagtcc---ctagat---ttttgttctttgagtttggagaattgatttgttcccttatttataatttcaaaaattattccttgtttaaagtaaatgtgcaacttattttggaatcataaaaattaagcacataattacatcgatttatctcatctaggttcttgcttttatcatgttatgtgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGTTCCAAAAGTTTTATTGCTAAG
||| | || ||  |     |||    | |||    ||   | | |    ||||    |  | || | |  |||| | |  | |  || |   ||||        | ||| | |   || |||||   ||||| |     ||     |||     || || | ||   |    |        || | || |   |  | |||   |||| || || || || ||| | |||||||| ||||||  ||| |||||||||||||||| ||||||||| |||
gtacgctttctctttcttttcctgttttgatacaattcagtatatcttcttggcatttgaagttttacttttatctgtcttattgaagaaagttccaga---ggactaattttattacctatttca-aatcaaacttgctacatctataccc-tattgagtaatagtaaagcgaactgactttatttctttgaaaatatga-ttagGTTTGCCTATCTAAAGGTATAGGTGCTCCAGTTGGATCTGTTATTGTTGGTTCCAAAAATTTTATTGCCAAG
















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|161719590|gb|FC069398.1|FC069398
EST:     CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG                         GTATGTCTCTCAAAGGTTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
genomic: CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCGgtatgattcc ... tgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
EST: gi|30300481|gb|CB977275.1|CB977275
EST:     CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG                         GTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
genomic: CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCGgtatgattcc ... tgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
EST: gi|110379523|gb|EC944723.1|EC944723
EST:     CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG                         GTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
genomic: CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCGgtatgattcc ... tgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
EST: gi|110727225|gb|EE103744.1|EE103744
EST:     CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG                         GTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
genomic: CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCGgtatgattcc ... tgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
EST: gi|110362584|gb|EC926127.1|EC926127
EST:     CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG                         GTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
genomic: CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCGgtatgattcc ... tgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGT
EST: gi|29785385|gb|CB342317.2|CB342317
EST:     CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG                         GTATGTCTCTCAAAGGGTTTGGGTGCTCCCG
genomic: CACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCGgtatgattcc ... tgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcgatttatctcatctaggttcttgcttttatcatgttatgtgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGTTCCAAAAGTTTTATTGCTAAG
                              ttttatcatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattcctaatgggagtccctagatttttgttctttgagtttggagaattgatttgttcccttatttataatttcaaaaattattccttgtttaaagtaaatgtgcaacttattttggaatcataaaaattaagcacataattacatcgatttatctcatctaggttcttgcttttatcatgttatgtgtgagccagGTATGTCTCTCAAAGGGTTTGGGTGCTCCCGTTGGAAGTGTGATTGTTGGTTCCAAAAGTTTTATTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG