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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

Basic information

species Vitis vinifera
transcript Vv08s0007g07420.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
--tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggc-ccatgtgtttatatggtgt-tttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
    | ||||| |    | ||  |    | |||  || ||| |  ||      |  ||  | | |   | ||   | || |    |  | | |  | ||   ||||||||| || || ||||||||||||||||| |||||||||||||| |  || |||||||| || ||||||||||||||||||||||| ||||||||| |
ttctactctcaactg--tctggactccaatttt--tcctgtgagcttctggtgtccttccattagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 14
----tcagtctcatccaaatttgat-catggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
      | |  | | ||  ||  |  ||   | | |  |||| |  |  || ||  ||   ||| | ||   | ||  | | |||||| |||    |  |   |||||||||||| || || ||||| |||||||| |||||||| |||||||| |||||||| || ||||| ||||||||||| || ||||| ||||| |||||
gtatatattgacttgcatgttccacacacttagtgtt-tcttttgtttatgtattatgacatgaatggggtta-gt-ctgacatggtgattt--actctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCAAATGGATCAACAAGAAATGGAAAGAAGGATTTCATGTTACATCAATGAC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
------------------------------------------------------tcagtctcatccaaatttgatcatg-gaatttaatcttgtcatgttgcatattgttttgagttggccca--tgtgttta--tatggtgttttctgt---ttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
                                                         |  | ||||| || |  ||||  | | |||||| | |  |    |    ||  || |  ||||  |  |||| | |  ||| || |  | |||   ||||   |||||| |||||  |||| ||||||||||| || ||||| || || ||||| || ||||| ||||| ||||||||||||||||| ||||| ||||||||| |
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtt-tcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 9
tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgt---tttgagttggcccatgtgtttatatggtgttttctgtttatgtt-----agGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
         ||  |||   |||      || |  |  ||    | ||  |||     |  | |   ||    ||  | || ||| ||  | | |||    |     |||||||||||| |||||||| |||||||| || ||||| || ||||| |  || |||||||||||||||||||||||||| |||||||| ||||| ||| |
--------gtcataatgcaatctctattttaagccccgttgcatcgcgcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAGCAATCATACAAGGTTAGTGAGTCGTTTCCTTACAAGTGGATTAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 10
tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgt---tttgagttggcccatgtgtttatatggtgttttctgtttatgtt-----agGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
         ||  |||   |||      || |  || ||    | ||  |||     |  | |    |    ||  | || ||| ||  | | |||    |     |||||||||||| |||||||| |||||||| || ||||| || ||||| |  || ||||| |||||||||||||||||||| |||||||| ||||| ||| |
--------gtcataatgcaatctctattttaagcctcgttgcatcgcgcattaactatcagggcctacgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAGCAATCATACAAGGTTAGTGAGTCGTTTCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 14
-----tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
      |  |   ||  |  ||||  | ||    |  | | | |||  ||||    |  | ||  | |    || |||  ||      ||||   ||| ||  |||||||||||| || |||||||| |||||||| |||||||| || ||||  || ||||| || ||||| |||||||||||||| ||||| ||||| |||||
tttctgcgattctatagatgtttggcc-tgtctctgtaccctttcactttgc---cttgtctgcatcgatttatctgtgcattaaacctttttactttttgc-agGAACTCCTTACACTCAGCAGTCTTACAAAGTTAGTGAATCATTCCCCTACAAGTGGATCAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGAC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
tcagtctcatccaaatttgatcatggaatttaatcttgtcat--gttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
   |||  || ||| ||  ||  |         |    ||     ||   |||  |  |  | |     ||   ||    |  | | || |   ||    |||||||||||| || ||||| |||||||| || || ||||| || || |  || ||||| ||||| |||||||||||||| |||||||| ||||||||| |
--tgtcctatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgt---tttgagttggcccatgtgtttatatggtgttttctgtttatgtt-----agGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
         ||  |||   |||      || |  | |||   || ||  |||     |  | |   ||    ||  | || ||| ||  | | |||    |     |||||||||||| ||||| || |||||||| || || || || || || |  || ||||| |||||||||||||||||||| |||||||| ||||| ||| |
--------gtcataatgcaatctctattttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
---tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
   |    ||| |  || ||   | ||| ||   |         |  | || | | || ||| ||      | |  | || |  ||  | || |   |  ||||||||||||| || |||||||| ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| |||||||| || || |||||
tattttagctcgtttaacttctgtgatgaaaggaacatcaactgttcttcagaat-ttatgactttatatttat-ctcatgtt-tgaatcctttactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
----tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
      |||| | ||  |   | |   ||  | | || ||| |  || | ||||  |  |  |    |||  | |  ||||      |  | |  |   | |||||||||||||||||||||| || |||||||| || || || ||||| || || ||||| ||||| ||||||||||||||||| ||||| ||||| |||||
gtcggtagtcacgtctcatgataactttgccaatgaa-cttat--tgattcataaagcatgaaa---gccgttttacttattccacttcatgtaat-gcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
----tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
      ||||   |  || |||  | ||    |||||| ||    | |    ||||  | ||| |   |      | | || |   | ||| ||| | |   ||||||  | ||||| ||||||||||||||||||||||| || ||||| ||||| ||||| |||||||| |||  |||||| ||| | || ||||||||| |
cgtcatagtcctttttaattttagttattt--tttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattt-tgtgt-taacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------------------------------------tcagtctcatccaaatttgatcatggaatttaat--cttgtcatgttgcatattgttttgag-----ttggcccatgtgtt------tatatggtgttttc---tgtttatgt---tagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
                                                  |   |||||      |||||| ||  | | | ||   ||||||| ||| | |   ||||| |      |||| | ||| ||      |  ||| ||| |     ||||||| |   |||||||  | || || |||||||| ||||||||||| || || ||||| ||||| ||||| |||||||| |||  |||||| ||  | || || || ||| |
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcat-ttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

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|110363759|gb|EC927370.1|EC927370
EST:     TCAATAGCAGGGGCTGCTAATGGGAGTTCTTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: TCAATAGCAGGGGCTGCTAATGGGAGTTC-TTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|34544477|gb|CF512709.1|CF512709
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|110379519|gb|EC944719.1|EC944719
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|37190348|gb|CF609697.1|CF609697
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|22012560|gb|BQ797594.1|BQ797594
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTCA
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTA
EST: gi|37190390|gb|CF609739.1|CF609739
EST:     CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGCCATGTCTAAAG                         GAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCC
genomic: CTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgttggatcac ... tttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
                                      ttttctgttt  CT-rich tract
                         tgtttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - tcatcca
- - - - - - - - - gatcatg
- - - - - - - - - - - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccatgt