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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTAAGACAGAAGAATGGGAAGTATGGAGTTGGTGGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattttacatttggtgaggttcataagctaaatttagtcacttcaacattcatattactgctaaggcatatacatttggtgggttttctgtgcta...

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G39870.2 (Glycine max), 5'ss of exon 13
ATACTAAGACAGAAGAATGGGAAGTATGGAGTTGGTGGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattttacatttggtgaggttcataagctaaatttagtcactt-caacattcatattactgctaaggca-tat-acatttggtgggttttctgtgcta
 || | ||||||||||  ||||||||||| |||| ||  |||||||| || ||||||||||||||||| |||||||| |||||||||||||| ||||  |||| || ||   |||     |  | || |   || ||   |   || | |||||    || ||| | |   |||   | ||||  | | 
GTATTGAGACAGAAGAGAGGGAAGTATGGTGTTGCTGCCATCTGCAACGGGGGAGGAGGAGCATCTGCTCTTGTTCTTGAGCTCATgtaagcctttttaattttgtcag--ccattgttcagttataatagtttacagtgtagttaatcctgcttgaacaatatgagaccaggtccatattctcgggt-

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 14
ATACTAAGACAGAAGAATGGGAAGTATGGAGTTGGTGGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattttacatttggtgaggttcataagctaaatttagtcactt-caacattcatattactgctaaggca-tat-acatttggtgggttttctgtgcta
 || | || |||||||  ||||||||||| ||||  |  ||||||||||| ||||||||||||||||| |||||||| |||||||||||||| ||||  ||||||| ||   |||     |  | || |   || ||   |   || | |||||    || ||| | ||  |||   | ||||| |   
GTATTGAGGCAGAAGAGAGGGAAGTATGGTGTTGCCGCCATCTGCAATGGGGGAGGAGGAGCATCTGCTCTTGTTCTTGAGCTCATgtaagcctttttaatttggtcag--ccattgttcagttctaatagtttacagtgtagttaatcctgcttgaacaatatgagatcaggtccttattctgggga-
















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|30301836|gb|CB978630.1|CB978630
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTTTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGCCATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|30301768|gb|CB978562.1|CB978562
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|30329769|gb|CD013031.1|CD013031
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110414965|gb|EC980831.1|EC980831
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|34362568|gb|CF404153.1|CF404153
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110358833|gb|EC923335.1|EC923335
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTTTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|34545214|gb|CF513446.1|CF513446
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110381509|gb|EC934651.1|EC934651
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|30298600|gb|CB975394.1|CB975394
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110376548|gb|EC941608.1|EC941608
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|34546208|gb|CF514440.1|CF514440
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|27585769|gb|CB008464.1|CB008464
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110378421|gb|EC943552.1|EC943552
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110395476|gb|EC961142.1|EC961142
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
EST: gi|110361851|gb|EC925352.1|EC925352
EST:     GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCAT                         GCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC
genomic: GGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattt ... catgttgcagGCCAGTTGCAAGGTTGGGACATTCCAAGTTATGAAGAAATTGAGTTGTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACTAAGACAGAAGAATGGGAAGTATGGAGTTGGTGGTATCTGCAATGGTGGAGGAGGAGCATCTGCCCTTGTTCTAGAGCTCATgtaagcattttacatttggtgaggttcataagctaaatttagtcacttcaacattcatattactgctaaggcatatacatttggtgggttttctgtgcta

- - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA