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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 9
agcatacttactgaattgataattta---agccccatcttacttgct-ttataacattgtaaccttcaattctcatcttttgtttttttcttttgt-tgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG
     ||| ||||| ||  |  | |    | ||   ||| | ||| |  |  ||   | || |  |      |||| | |  |     ||||| || ||||  ||||||||||| |||||||| ||| |||| |||||||| ||||||||||||||||||||||||||  ||
----cactaactgacttctttttctgtctacccatttctaaattgatgcttgaatgctttatcagttgtccatcatttctc-tcacagtctttggtgtgtttcagTGGTGAACCCTTGACAGTCCAGTCTCCAGGAACACAAACTCGCAGTTTCTGCTATGTCTCTGATCTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 9
agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgt-tgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG
   |   | |||   ||     | |   |||||| |         | |   ||||     |    |   | || |||   |   ||||| || ||||  ||||||||||| |||||||| ||| |||| |||||||| ||||||||||||||||||||||||||  ||
-taactgtgacttctttttctgtcttctccccatttctaaattgatgttttattgctttatctgttatccgtcatttcgctcaatctttggtgtgtttcagTGGTGAACCCTTGACAGTCCAGTCTCCAGGAACACAAACTCGCAGTTTCTGCTATGTCTCTGATCTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 9
-----agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG
     |  |   | | | | ||||  | | |      || ||  || |  | | |  ||| |  ||  |  | |    | |  | |  || |||    ||| |||||||||||| ||||| || || | ||| ||||| || ||||||||||||||||||||||||||||||
attcaaataccttgatttagttgaccactcataatttatttt-tttaccatttcaagttgcactctctatctgttgcttctcatataatttttt----gttatagTGGTGAACCCTTGACTGTCCAAGTTCCAGGAACTCAAACTCGCAGTTTCTGCTATGTCTCTGACATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 8
--agcatacttac--tgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG
      ||  |||  ||| ||  | | | |       ||||  || |  | | |  ||| |  ||| | || |    | |    |     |||   ||||  ||||||||||| || || || || | ||| ||||| || ||||||||||| ||||||||||||||||||
ttgatttaaataccttgatttagttaatcataatt--tcttttttaccatttcatgttggactctttatttgttgcttctcacataaaattttg--tgttacagTGGTGAACCCTTAACTGTCCAAGTTCCAGGAACTCAAACTCGCAGTTTTTGCTATGTCTCTGACATG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 10
agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttctt--ttgtt-gttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG
   ||  | | |    |||| |  || |     | || ||  |||  |   ||| | |  ||  ||||| | | ||   || |  | |  | |||  || ||| || ||||| |||||||| ||   ||| |||||||| ||||| ||||||||||||||||||||| ||
--tattttaattttggtgattagctatgttttctatttctgtcttagtcctatttttatatt-gattcttacccttcaattctcacataatggttcattatagGGGGGAACCATTGACAGTCCAATGTCCAGGAACACAAACTCGAAGTTTCTGCTATGTCTCTGACCTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 8
---agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG---------------------------------
   ||| |  || || |||  |      ||     || || |  ||| || |  | |        ||  |||  | | ||||| || || |   |  ||  || |||||  | ||||| ||||||   || || |||||||||||||||||||| ||||| |||||||||                                 
gtgagcctctttgctcaatccaacgaacaaattttattttccgagctataaattact--------catctcttgt-tattgttcttgtcatgaatactt--agGGGTGAGGCATTGACTGTTCAGAAACCAGGGACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGAT

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 8
agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgt-tgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG---------------------------------
                | |     | ||| |  ||  ||||  || | | ||   |    ||||  |||  |    ||| |||   ||   | |||||||| |||||  | ||||||||||||   || || |||||||| ||||||||||| |||||||| ||||||                                 
---------------gtaaagtcattagctctctca-acttcattgaaaccaagttttgtttcatctctgcttagctgtgtttccattaaatgtgttgtagGGGTGAGGCATTGACAGTTCAGAAACCGGGGACACAGACCCGCAGTTTCTGTTATGTCTCCGACATGGTGGATGGACTTATCCGTCTTATGGAAGGCAAT

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|71885522|gb|DT034577.1|DT034577
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         TGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         TGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
EST: gi|71888765|gb|DT037820.1|DT037820
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         TGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         -GAGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCT
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTG-GTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCT
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         TGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
EST: gi|56408375|gb|CX016627.1|CX016627
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         TGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTG
EST: gi|33406260|gb|CF211887.1|CF211887
EST:     AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG                         TGGTGAACCTTTGACAGTTC
genomic: AATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtcctt ... gttgttgtagTGGTGAACCTTTGACAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataacattgtaaccttcaattctcatcttttgtttttttcttttgttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG
       ttgtaac  putative branch site (score: 2)
             ccttcaattctcatct  CT-rich tract
                            ttttgtttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatacttactgaattgataatttaagccccatcttacttgctttataacattgtaaccttcaattctcatcttttgtttttttcttttgttgttgtagTGGTGAACCTTTGACAGTTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG

-gcatact
- - - - - - - - - - - - - - ccccatc
- - - - - - - - - - - - - - - - - - tacttgc