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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGAGATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctttcacccttgctctccctcatccatattggataatatatgtatgtagagatgtctcatttgtcttctcttcttgccag

Basic information

species Vitis vinifera
transcript Vv13s0019g02360.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os05g38150.2 (Oryza sativa), 5'ss of exon 15
AGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGAGATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactct----ctttcacccttg-ctctccctcatcc-ata---------------ttggataatatatgtatgtagagatgtctca----tttgtcttctcttcttgccag
| |||   || |||||||||||||||| ||| ||||| |||||||||||| ||||||||||||| || || || ||||| |||||||| ||  |||||||| ||        | | || | || ||| |||| |||| |||               ||  | || | |||    |  |  |  | ||    |   | |||| |   |  |||
AAGCTGTTTCATTTCATCATGAGTATAGTTCTATGGCCTGCACTGTTGAGTTTGTTGATGATGTTCAATCAGCAATTGACCATATTCATCGTTATGGAAGgtacctaatagttgtgactcctgtctcccccttatcccatagtactagttgttttcttaaacaaaaaatgagattcaatgtaacccaaatttccatattctatctgtttcag

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 16
AGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGAGATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactc--tctttcacccttgctctccctcatccatattggataatatatgtatgtagagatgtctcat-ttgtcttctcttcttgccag---------------------------------------------------
|||   | || ||||||||||||||||| |||||||| |||||  | ||  ||||||||||||| || || || ||||| |||||  | ||  |||||||| |  |  | |||| || |       |||||||  | ||   |  |  | ||||| ||   |    | |  | | | | | || |  |                                                     
AGGTAGATTCATTTCATCATGAGTATAACTCAATGGCATGCACCCTCGAATTTGTTGATGATGTGCAGTCAGCAATTGACCATATAAATCGCTATGGAAGgtatgcagtttttctccatactatatcctcatcactttttttttttggaagtatgcagtttttctccttactatatccccatcatttcttttttttttttttgaactaaacttgattgtgttaaatatatgttcatttcag

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA02G41850.1 (Glycine max), 5'ss of exon 13
AGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGAGATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctttcacccttgctctccctcatccatattggataatatatgtatgtagagatgtctcatttgtcttctcttcttgccag--------------------------------------------------------------------
| || ||  | |||||||||||||| | |||  |||||||||||||||| ||||| ||||| ||  || | || |||||||||||  | |   ||||||||||      |     ||| ||       |  ||| ||| |  |||| |   | |  |  |||||  |||| ||  | | | |  ||                                                                     
AAGCACAAACATTTCATCATGAGTACAGTTCGCTGGCTTGCACTGTTGAAATTGTGGATGACGTGTATGCAGCTATTGATCATATAAATCTTTATGGAAGgcatgtcactgttttctt-cttgataggaaacatgttgaaatatattttggtttc-atttgtcttctttg-ctcttgtccatttcaattgacatctatgttagtgtagtgaacttagatggaaaagtgtcatatattctctttcttttatggcag

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA14G07120.1 (Glycine max), 5'ss of exon 13
AGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGAGATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctttcacccttgctctccctcatccatattggataatatatgtatgtagagatgtctcatttgtcttctcttcttgccag---------------------------------------------------------------------
| || || || |||||||||||||| | |||  |||||||||||||||| ||||| ||||| ||  || | || ||||| |||||  | |   ||||||||||      |     ||| |||      |  ||| ||| |  |||| | |   |  |  |||||  |||| ||  ||| | |  ||                                                                      
AAGCACATTCATTTCATCATGAGTACAGTTCGCTGGCTTGCACTGTTGAAATTGTGGATGACGTGTATGCAGCTATTGAACATATAAATCTTTATGGAAGgcatgtcactgttttctt-ctcgataggaaacatgttgaaatatattt-tgctttcatttgtcttctttg-ctcttctccatttcaattgacatctatgttagtgtagtgaacttaggtggaaaagtgtcatatcttctcttttcttttatggcag

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|110364352|gb|EC923948.1|EC923948
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|29783366|gb|CB349487.2|CB349487
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|30297817|gb|CB974611.1|CB974611
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110427351|gb|EC993787.1|EC993787
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|33402185|gb|CF207812.1|CF207812
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|33402196|gb|CF207823.1|CF207823
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110377214|gb|EC942273.1|EC942273
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110365796|gb|EC929255.1|EC929255
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|33402539|gb|CF208166.1|CF208166
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|32461077|gb|CD802251.1|CD802251
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110362804|gb|EC926359.1|EC926359
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110382148|gb|EC938618.1|EC938618
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110375487|gb|EC940476.1|EC940476
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110420384|gb|EC986656.1|EC986656
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110388887|gb|EC953685.1|EC953685
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|33402105|gb|CF207732.1|CF207732
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|29783302|gb|CB349405.2|CB349405
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110414936|gb|EC980800.1|EC980800
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
EST: gi|110421820|gb|EC988122.1|EC988122
EST:     ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAG                         TGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT
genomic: ATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctt ... ttcttgccagTGCACACACCGATTGCATCATTGCAGAAGACCTTGAAGTTGCTGAAGTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGAGATTGTTGATGATGTACATTCTGCCATTGATCATATTCACCGACATGGAAGgcactctctttcacccttgctctccctcatccatattggataatatatgtatgtagagatgtctcatttgtcttctcttcttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG