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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcatgctaaatctcttacttgaattaagcttcctaatcttttaataaattcaccttttgttccattttaaatgtctcaaaccttgattttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA

Basic information

species Vitis vinifera
transcript Vv16s0013g02020.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 3
cttcatgctaaatctcttacttgaattaag-cttcctaatcttttaataaattcaccttttg--ttccattttaaatgtctcaaaccttgattttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA
           |  | | |||| | | |   ||| | ||  |  | || ||       | ||  |||||||    |  |      | ||| |||  |    |||| ||||| ||||| |||| |||| | ||| | || |||| |||||||| ||||||||| || |||||||| ||||||||| ||||||||||||| ||||
---------gtacatttcactttactgagatctttcaaagatgattatcaacaatgtatctgccttccattaatgacttggttttctttggtttaatg--cagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGTGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 3
cttcatgctaaatctcttacttgaattaagcttcctaatcttttaataaattcaccttttgttccattttaaatgtctcaaaccttgattttgttgt-tagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA
    ||  |  || ||  ||| | ||   ||     |       || || |||| ||  | || ||||   |||  ||      |   |    |  | ||||| ||||| ||||| |||| |||| | ||| | || |||| ||||||||  |||||||| || |||||||| ||||||||| ||||||||||||| ||||
--gtatatttgatttc--actgggatcttgcggaagatggcaaaaaaaatttcagctgct-tttcatt---aattcctttgttttcattggcttaatgtagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGCGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G084757_T02 (Zea mays), 3'ss of exon 2
cttcatgctaaatctcttacttgaattaagcttcctaatcttttaataaattcaccttttgttccattt--taaatgtctcaaaccttgattttgttgtt-------agGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA
           ||   | | |||| |  || ||  |||     ||  |     |  |||  | | | ||  ||    |  |  | || | | |||||  |       |||||  ||| ||||| |||| |||| | ||| |||||||||  || |||| ||| ||||| ||||||||||||||||||||| | ||||| ||||| ||||
---------gtatacttgaattgagtcgagatta-taacaagatagcatgaggat-tttcatcctagttagtactgatgccttatctcgctcttgttactgaacaacagGATAGCACCTACAAGTACTTTGAGATCATCCTGGTTGATGTGGCCCACACTGCCATCCGCAACGACCCAAGAATCAACTGGCTATGCAATCCTGTGCACA

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 3
cttcatgctaaatctcttacttgaattaagcttcc--taatcttttaataaattcaccttttgttccattttaaatgtctcaaaccttgatt--ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA
 |  |    |||||| | | |||     |||||     ||  |   |  | | |   | |       | |    ||| || |   | |  ||  |       |||||  ||| ||||| ||||  ||| | ||| |||||||||  |||||||  || ||||| ||||||||||||||||||||| | ||||| ||||| ||||
gtatacttgaaatct-tgaattgtgccgagcttataacaagatagcatgagaattttcatcctagttagtactgatgccttatctccttgttactgaacaacagGATAGCACCTACAAGTACTTCGAGATCATCCTGGTTGATGTGGCTCACACCGCCATCCGCAACGACCCAAGAATCAACTGGCTATGCAATCCTGTGCACA

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 3
cttcatgctaaatctcttacttgaattaagcttcctaatcttttaataaattcaccttttgttccattttaaatgtctcaaaccttgattttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA
        || || |  ||| |   || ||    ||  || ||||    |||   ||  |     ||||||| |    ||    ||  |||  ||  |||||||| || ||||| ||||| ||| | |||||||||||  | || ||||||||| | || || ||||| |||||||||||||||||||| || || ||||
-------gtacatttactaccttctttcagtactctt-tcgtttaggtgattattctggttagatattttaacttgtcca----tt--tttctttaatagGATTCGACCTACAAGTACTACGAGATCATCTTGGTTGACCCAGCACACAATGCTGTGCGTAATGACCCGAGAATCAACTGGATCTGCAACCCAGTTCACA

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|77577251|gb|DV217329.1|DV217329
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
EST: gi|110688477|gb|EE067077.1|EE067077
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
EST: gi|77584870|gb|DV221515.1|DV221515
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
EST: gi|77585149|gb|DV221663.1|DV221663
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
EST: gi|71876495|gb|DT025550.1|DT025550
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
EST: gi|77584906|gb|DV221536.1|DV221536
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
EST: gi|351023690|gb|FQ448241.1|FQ448241
EST:     GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAG                         GATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT
genomic: GACGGAAGCTGGGTGGTCTCAAGGTTCTCAACTCTTATTGGATCAATGAGgtctgtatag ... ttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaattcaccttttgttccattttaaatgtctcaaaccttgattttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA
                                           ttttgtt  CT-rich tract
                    attttaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcatgctaaatctcttacttgaattaagcttcctaatcttttaataaattcaccttttgttccattttaaatgtctcaaaccttgattttgttgttagGATTCCACTTACAAATACTATGAGGTAATCTTGGTTGATGCTGCTCACAATGCTATCCGGAACGACCCAAGAATCAACTGGATCTGCAAGCCTGTCCACA

- tcatgct
- - - - - - - - - - - - - - -gcttcct
- - - - - - - - - - - - - - - - - - - - - - aataaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacct