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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC

Basic information

species Vitis vinifera
transcript Vv18s0072g00630.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g64700.2 (Oryza sativa), 3'ss of exon 5
tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcct--cccccttgtttc-agGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
                      |||   |    |  | |     |   ||  || |  | |   ||| ||| ||| | |    |||  | |  |  |||| ||||||||||||||||||||||| || ||||||||||| |||||||| || ||||||||  ||  | || | |     ||  | || |||  ||| ||  ||
---------------------gtaattatcatgttcattgaagatggttattttccattttgcttgtttcataatatataaaccctagcactgtcatttccagGTCAAATTTCCTTGGCACAAAATTTATAATTTATGACACACAGCCCCCTTACAATGGGGCTGTAGTCCCTCACGTCGGAAGGACCAGCAAGAGATTTAAC

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g36190.1 (Oryza sativa), 3'ss of exon 4
tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttc-agGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
           || | || || |  ||  ||  |  |  ||   ||        | |   |   ||   ||||      ||||  |  |  |  |||  |||||||| |||||||||||||| || ||||| ||||| ||||||||  | || |||||  ||  | || | ||   ||| || |  ||||| || ||| ||
---------gtaactgtt-ttgtgtgcagatggtacacctttccttt-cgctccatttatttgatgatacaaaccaaccttgttgtgtctttcatttttagGTCAAACTTCCTTGGCACAAAATTTATAATCTATGACACACAGCCCTCTTATAATGGGGCTGTAATCCCTCCTGTTGGACGGAGCAGCCGAAGATTCAAC

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g59130.1 (Oryza sativa), 3'ss of exon 4
-----tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
       |     | ||    |  | ||   || | | | |        | ||     |      ||  ||  | | ||| ||    | | ||    | || ||||||||||||||| ||||| || ||||| || ||||| || ||||| |||||||||| |     ||| | | |||  |  || ||||||||  |||||| |
gtaaagttcctttgccatcaatcttcttgcacccacattgt----cacatacacgtggtcacagatacatgcataataatctgac-atacaccatggtattgcagGTCAAATTTCCTCGGCACCAAATTCATCATCTATGACACGCAGCCTCCATACAATGCTCGGACACTTTGCTCACAAGAACGGACGAGCCGTCGGTTCTCC

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g06420.1 (Oryza sativa), 3'ss of exon 4
-tatt--tcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
 ||||   | |   ||  |      | |    | ||  ||     | || ||  |  | |   |     |   || || | |   |  |        ||  |||||||| |||||||||||||||||  |||| |||||||| ||  | || |||||||   ||      || |   | ||   ||| ||||| || |||| |
gtattaacccgaagaaactacaaccttatttcagaacttaccccattttaatctaaaaattattgctgctgctaatatgtctccattttga-----attgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 4
tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
      |   |     | | || ||   |  |   |  ||| | |||| || | ||  | | |   |||  | || |||| ||   |        |||||||||||||||||||||||||| ||  |||| || ||||| || || |||||||||||  ||   |   |     | ||   ||| || | ||| ||||||
----gtactgctgcactggcttcaa---tgaacattgttttattttcagaattgacagtattttaatct-gacatatgtt-gttgccttttggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATACAATGGAACTAGTCAAACAGTGGCAGGGAAAACAAGTCAGAGATTCTAC

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G09030.1 (Glycine max), 3'ss of exon 3
tatttcaggtcaatttttgttttaagcctataatctag---tttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC---
  ||  |   | ||| ||           ||  || ||   |   |||    |  || ||  | || |      |  | ||| |      |||||  ||||||||||||||| |||||||| ||||| |||||||||||||||||||| || || ||   | |||| || || || || |||||||   |||| ||||| ||    
--ttctaataccattatttccccctattaatgttcaagaaatcactgtctgcatttttctggcaatataaacttat-tctgtatcaatctcccctcatttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCTCAGCTGTCTCCTCCAGGCCGAA---GCCGTAGGTTTTATTCA

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G30660.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------tatttcaggtca---atttttgttttaagcctataatctagtttgtgtt---cataaattactctctatctgtctcaaaatt------------tgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC---
                                                                             || | |||  |   ||  ||||||||  || |||||| |   |||  |    || ||||  |      || |||    |||            ||| |  | | | ||| |||||||||||||||| |||||||| ||||| ||||||||||||||||| || || ||| |   | ||   || || ||||||||||| |   |||| ||||| |     
gtaagacttaatttttggtactcttttgggacctacttgacattcattttgcactaacaatcattgaattgtataagatctaaggctatgcataattgttttagacc-ataatccaaggtgttctagaaatcaattgtttctgtactttcttgtcattatgcacttatactgtattacattctcctggtttcagGTCAAATTTTCTTGGCACCAAGTTTATAATTTATGATACACAACCTCCCTACCACAATGCTATGCTGTCTCCACCTGGCCGCA---GCCGTAGGTTTTCAAAA

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G28200.2 (Glycine max), 3'ss of exon 4
tatttcaggtca--atttttgttttaagcctataatctagtttgtgttc-ataaattactctctatctgt-ctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC---
  | | |   ||  |||||    |    |   | |   | |   |||||   |  || ||  | || |   || | | | |||   ||   |||||  ||||||||||||||| || ||||| ||||| |||||||||||||||||||| || || ||   | |||| || || || || |||||||   |||| ||||| ||    
--tctaataccattattttcccctattactgttcaagaaatcactgttctgcatttttctggcaatataaacttatactgtgtcaatct--cccctcatttcagGTCAAATTTTCTCGGCACCAAGTTTATAATTTATGATACACAGCCTCCCTATAACAATGCTCAGCTGTCTCCTCCAGGCCGAA---GCCGTAGGTTTTATTCA

upper sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G36940.2 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------tatttcaggtcaatttttgttttaagcctataatctag---tttgtgt------tcataaattactctctatctgtctcaaaatttgtttgtcct---------cccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC---
                                                                             ||| | |||  |    |  || |    | |||||| |     |||||       |||    || || |   |   | |||  || |  || | ||             ||||||||||||| ||||| |||||||| ||||| |||||||||||||| || || || |||||   | ||   || || ||||||||||| |   |||| ||||| |     
gtaagacttaattttgggtactcgtttggggcttacttgacattcatttttgcacttacaatcattgacttgtataatatcttaggctatgcataattgtttttccataatccaagaagttgtgcaagaaatcaattgtttctgtgctttcttgtcatgatgtacttatactatattacatttttcttgtttcagGTCTAATTTTCTTGGCACCAAGTTTATAATTTATGATACGCAACCTCCCTACAACAATGCTATGCTGTCTCCACCTGGCCGCA---GCCGTAGGTTTTCAAAA

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|110732567|gb|EE107967.1|EE107967
EST:     GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAG                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
EST: gi|71865477|gb|DT014532.1|DT014532
EST:     GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAG                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
EST: gi|110360670|gb|EC923961.1|EC923961
EST:     GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAG                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
EST: gi|110378812|gb|EC943963.1|EC943963
EST:     ATGCCGATAAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAG                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: ATGCCGAT-AACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
EST: gi|110378995|gb|EC944161.1|EC944161
EST:     GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAG                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
EST: gi|34546578|gb|CF514810.1|CF514810
EST:     GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAG                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
EST: gi|110731881|gb|EE106679.1|EE106679
EST:     GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAA                         GTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA
genomic: GATGCCGATAACATATCAAGATCAAGCAGCACTTATATTGGGAAGCTGAGgtagatgaat ... cttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
                             tttgtttgtcctcccc  CT-rich tract
                         aaaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC

- - -caggtca
- - - - - - - - - - -ttaagcc
- - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaaaa