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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT

Basic information

species Vitis vinifera
transcript Vv04s0023g03860.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctt---tggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
           || |  || || |  |  | | |  ||||    |      ||||  || |   | |    | | ||| | ||      |   ||||| |||||||||||||||||| |||||||  |||||||||| || || ||||||||| |  |||| ||||| || |||||||||||||||||||| |||||
-----------gtaatctggttgcgctgctatct--aattctgcatgcttgttttc-ttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 2
----gtagct-tcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatgg----ctctgaatttgttctct----ttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
      |||| ||  | |   ||  ||   |  || |   |  ||  |    | | ||||   |  |||||         |||| ||  ||| |     ||   |||| || ||||||||||||||| |||||||  |||| ||||| || || ||||||||  |  |||| ||||| || ||||| |||||||||||||| |||||
gtgaccagctatcctattttgttactttgatgcttttcccccctttgtgcatatcctttttccttgtttatcaaaatggttgaacttcatctttgcaactgccgcagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 2
-----------------------gtagcttcacagtcact-tgtttccttttttgttttcaattactaacaaacattttgattatttt-----atggctctgaatttgttctc---tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
                        |  | |   | | |   || ||  |||||  ||| |  |     | |  | ||||  || ||       |||| |  |  |   |  |      || || ||| || ||||||||||||||| |||||||  |||| ||||| || || ||||||||  |  |||| ||||| || ||||| || ||||||||||| |||||
gtgactagccgtgctgttctgtcctgtcctgctacttatgatgctttttttttcctttcctttgcgcgatatcctttttctttgttcatcaaaatggttgagcttccatctttgcaactgtaatagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAAGCCAGCTATGAGAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
           || |          || |||| |     |  |     |  ||   | | || | ||| | | | | |||| | | ||||||||| || ||||||||||||||||| |||||||||||||| || || || ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||
-----------gtaatgctgcgtgattattgtctctg--tgatgttggagcttggaagttttctctggattt-attgtgttatttgtggaacagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 3
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
           || |          || ||||||     |  |     |  ||   | | || | ||| | | | | ||||   | ||||||||| || |||||||| |||||||| |||||||||||||| || || || |||||||||||| |||| ||||||||||| ||||||||||| |||||||||||
-----------gtaatgctgcgtgattattgtttctg--tgatgttggagcttggaagttttctctggattt-attgtgttacttgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 2
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
                 |  ||  | |||| | ||     | |     |  ||  | |  |||||    | |    || |  | | ||||| ||| || |||||||| || |||||  |||||||||||||||| || || |||||||||||||| || ||||||||||| ||||||||||| |||||||||||
--------------gtattgttgttattttttctttgtccattctgggatgttgagttctttttagatttttattattctattatgtggaatagGTCAAGAGGATTATAATAGATTACGACCTTTGAGTTATCGTGGTGCTGATGTTTTCATATTAGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 2
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
              |||  | |  |||||| |||   | |  |     |  ||  | |  |||||    | |    || |  |   ||||| ||| || |||||||| || |||||  |||||||||||||||| || || |||||||||||||| || |||||||| || ||||||||||| |||||||||||
------------gtactactattattttttctttgtcaattttgg--gatgttgagttctttttagatttttattattttattacgtggaatagGTCAAGAGGATTATAATAGATTACGACCTTTGAGTTATCGTGGTGCCGATGTTTTCATATTAGCTTTCTCTCTGATTAGCAAGGCCAGTTATGAAAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 3
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
|||    |  | | |   |  || |  || ||  | |    |    |     ||||     | |    || |   |||||| |  |   |||||||||||||||||| |||||||| |||||||||||||| ||||| || ||||||||||| || ||||||||||| ||||| ||||| || ||||| |||||
gtactgactaaataatagggatcttacttagtagt-agcggcagctatgggatttgg--ggtctgaaacttttgttttgttgttgt--aaacagGGCAGGAGGATTATAACAGATTAAGACCTTTGAGTTACCGCGGTGCTGATGTTTTCATCTTAGCATTCTCTCTTATCAGTAAGGCTAGTTATGAGAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatt-tgttctct-ttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
          | | | |  |   |   ||  |  ||  ||  | | | |   |||  ||  |  || | ||  |||| |||| |   ||    ||||||| ||||| || |||||||| |||||||||||||| || || || |||||||||||  | || ||||||||||| || ||||| || ||||| |||||
--------gtaatgaatgatgatccaattcataatcc-ttggtgagaga-gctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 2
-gtagcttcacagtcacttgtttccttttttgttttcaattactaac---aaacattttgattat-tttatggctctgaattt-gttctctttgga-acagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
  | || ||| |    ||    |       |    ||||  |  | |    |||  | | ||||  ||| || |  || |  | ||| || ||| |  |||| || || |||||||||||| |  ||||| | |||||  | || || ||||| ||  || ||||||||||||||||||||||||| || ||||||||  |
tttcgcatcagaagt-ctcaccttacaccattcactcaaggaacagcctggaacgatcttattacatttgtgacgatggagatagttttcgttgaacgcagGTCAAGAAGATTACAACAGACTCCGACCTCTTAGTTACAGGGGTGCCGATGTGTTTTTACTGGCATTCTCTCTCATCAGCAAGGCTAGTTATGAAAACAT

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|110376013|gb|EC941052.1|EC941052
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|110713128|gb|EE088780.1|EE088780
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|110390015|gb|EC954898.1|EC954898
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|110396036|gb|EC961711.1|EC961711
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|87586594|gb|DY474807.1|DY474807
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|110404309|gb|EC969170.1|EC969170
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|33410493|gb|CF216120.1|CF216120
EST:     TGTGGTTGTCGATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG
EST: gi|110366542|gb|EC930452.1|EC930452
EST:     TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG                         GGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGTGGGGCAGATG
genomic: TGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcac ... tttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT
                                    tttgttctcttt  CT-rich tract
     acaaacattttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG