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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtgtgtatctgtcacaaccttttttatgtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG

Basic information

species Vitis vinifera
transcript Vv19s0090g01460.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g39310.1 (Oryza sativa), 3'ss of exon 1
agagtgtgtatctgtcacaaccttttttatgtgttattatatgcctattgcat--tctgatgcttggcctaatgtttccatgttcatgatttttttctgc-agTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG
||||  |  || || |   | |||  | |  || ||  ||||   || |||    |||  |  |||  |   | |||     ||  |  | |||     | |||||  |  |||||   || ||||||||||||||||| || ||||||||||| || |||||||| ||||| || ||  | ||||||||  | ||| |  ||
agag-ataaatgtgcccttatcttgctaa-atgctagcatat-tttactgctcggtctattcattgaaccttttttttttccttggtcgtgtttacgaaccagTGCAAGTACTGGAGTAAAGAGAAGAGGTGGTCCAGGTGGGCTAAACAAAGTCTGTGGTGTTTCTCCTGAGCTGCAAGCTATTGTTGGTGAACCAACCATG

upper sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 1
agagtgtgtatctgtcacaaccttttttatgtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAG--CTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG------
        ||     ||   |   |  | ||| || |  |||   |||     |  | | | |    | |   |  |   ||  |||||| | | ||   |  || ||  ||   |    || ||||||||| || || ||| |||| ||||||||||   ||||||||||||||||||||||||||||  || | ||  ||      
-------ctactcagcatgtcaactgatttgtattctactatag-tatcttggttcgtttccttttatgaaactgactgattagtgatttgtgtgtgatttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA

upper sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G035325_T01 (Zea mays), 3'ss of exon 1
agagtgtgtatctgtcaca-accttttttatgtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAA---AAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG------
        ||      ||  | | | |  |    ||  ||  |  |||| | ||  || | |||   || | | |  |   ||  |||||| | | |    |  || || ||   ||||   || ||||||||| || || ||| |||| ||| |||| |   ||||||||||||||||||||||||||||  || | ||  ||      
--------tactcactactcagcatgtcaactgatttgtacttcgctatagtatcttggttcttt-tctgaagctcactgattagtgatttgtgtataatttcttctag-

upper sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 1
agagtgtgtatctgtcacaaccttttttatgtgt-tattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG
  |||   |      || ||  || | | ||||| | ||| ||     ||   |  ||    | ||  |   ||     ||||  |  || | |  || ||| ||| | ||      || ||||||||||| ||||| ||||| | |||| | || |||||||| ||||||||||||  ||||||||||||||||||  ||
ttagtaatttataaacagaatattatgtctgtgtctgttaaatttgctttttttgttgcaattgggattggagtaatgctgtttttc-ttgtgtcttgtagTACTCAAACTAAGGTGAAGAGAAGAGGTGGCCCAGGAGGTCTCACCAAAATCTGTGGTGTTTCGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTG

upper sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 1
agagtgtgtatctgtcacaacctttt-ttat-gtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG
 |    |  ||   | ||||| || | |||| |||| ||||| |   | |    | |  |   |||||  |        || |      ||||  | ||||||||||  ||||||||||||||||  |||||||| || || ||||||||||| ||  | ||||| || |||||| |     |||||||  | || || || 
-gcacattgattcat-acaacgttctattatagtgtgattatttctttctgatctacctaaatttggcacatcaacgaaatttgtcaacttttcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGTCTGTAGGGTTTCTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTT

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|37186556|gb|CF605909.1|CF605909
EST:     GAACCCACTGGCGGCCCCGTTGCAGTCCCCGAGGCTCCGCCTCAAGAAAG                         TGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCA
genomic: GAGCCCACTGGCGGCCCCGTTGCAGTCCCCGAGGCTCCGCCTCAAGAAAGgtttgtttct ... ttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCA
EST: gi|110713078|gb|EE088682.1|EE088682
EST:     GAGCCCACTGGCGGCCCCGTTGCAGTCCCCGAGGCTCCGCCTCAAGAAAG                         TGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGT
genomic: GAGCCCACTGGCGGCCCCGTTGCAGTCCCCGAGGCTCCGCCTCAAGAAAGgtttgtttct ... ttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG
                   gcctaat  putative branch site (score: 3)
                                          tttttttctgc  putative PPT
                                   ttcatgattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtgtgtatctgtcacaaccttttttatgtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG

- - - - - - - -cacaacc
- - - - - - - - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcatg