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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttcaattgtacatattccatgttgttatcttaccatttgcagatacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g01180.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 3
------catttcaattgtacatattccatgttgttatcttaccatttgcagatacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG
       | | |  ||  | | |   | | |   ||| ||   |      | |||| | |  |||   |  || |  | | |    |||| |    | | || |||||| ||||||| || || |||||||| || || | ||| ||||||||||| |||||||| |||||||||||||| ||||| || |||||||||||||||
ggtgcagaatacttttaaaaaaaaatcttatccatatatttgtacagatggttacaaaaagcaatgattacctgacatgggt--gctttgta----tttgatctagGTACTGGAGACCCTTAGTAAAAATTGTGGTGAAAGTGTATTTCAGCAGATCGTTGAGCGAGATATCTTACATGAAATGGTTAAGATAGTAAAGAAGAAG

upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 3
-----catttcaattgtacatattccat-gttgttatcttaccatttgcagatacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG
      |    | ||  | | |    ||  |   ||  ||       |  | |||| | |  |||   |  || |  | | |   || |       | | || ||||||||||||||||| || || ||||| || || | ||| |||||||||||  ||||||| |||||||||||||| ||||| || ||||| |||||||||
aggtgtacaatactttaaaaaagaaaattatccatagatttgtgcaggtggttacaaaaagcaatgattacctgacatgggttctttgta------tttgatctagGTATTGGAGACTCTTAGTAAGAATTGTGGTGAAAGTGTATTTCAGCAGATCATTGAGCGGGATATCTTACATGAAATGGTTAAGATAGTGAAGAAGAAG

upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G09390.1 (Glycine max), 3'ss of exon 2
--catttcaattgtacatattccatgttgttatcttaccatttgcagatacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG
   |      ||  | | ||||    |  || | |   ||  ||   | | | | | |  || |        |   || | | |   ||| || | || |||| | |||| || || || |||||||| || || | ||| |||||||||||  |||| |  |||||||||||||| ||||| |||||||| ||||||   
aataaagtgcttccaaaaattcatattcattgtttgtgcaagtggtaaca-aaacactggttacctgacatggacattttgtatccaaatatt-tgatgtagGCACTGGAAACCCTTAGTAAAAATTGTGGTGACAGTGTATTTCAGCAGATCATTGAACAGGATATCTTACATGAAATGGTTAAAATAGTGAAGAAG---

upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G21380.1 (Arabidopsis thaliana), 3'ss of exon 3
catttcaattgtacatattccatgttgttatcttaccatttgcagatacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG
          ||   | ||     || |  || ||| ||     | |     | ||  |  || | ||   ||| |||  |||||    ||    |  |||  ||||| ||| | || || ||||| || |||| |||||  ||||  |||||||| || ||||| |||| ||| |||||||||||||| |||||||||
----------gtgagtgtttacctttttactcatacaatgctttggtt----ggat--tctctttattgtattgatcttctttgggggatt--ggttcagGCTTTGGAAACTTTGAGTAAGAATTGTGGCGAGAGTGTGTACCAGCTCATTGTTGACCGAGATATTTTACCTGATATGGTCAAAATAGTGAAGAAGAAG

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|161720688|gb|FC069937.1|FC069937
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|77587150|gb|DV222704.1|DV222704
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|110724482|gb|EE100348.1|EE100348
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|161716239|gb|FC066502.1|FC066502
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|161718465|gb|FC067304.1|FC067304
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|161708941|gb|FC060484.1|FC060484
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|161710321|gb|FC059835.1|FC059835
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
EST: gi|110721049|gb|EE097599.1|EE097599
EST:     AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT                         GTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT
genomic: AGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTTgtgagtattt ... tctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG
                                            ttctaat  putative branch site (score: 2)
                                          ttttct  CT-rich tract
                                tattttggaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttcaattgtacatattccatgttgttatcttaccatttgcagatacagagaataattgctgtcttaagttgttctattttggaattttctaatatagGTATTGGAGACTCTCAGCAAAAATTGCGGGGAGAATGTGTTTCAGCAGATTGTTGAGCGTGATATCTTACATGAGATGGTCAAAATAGTAAAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - catttgc
- - - - - - - - - - - - - - - - - - - - - -agataca
- - - - - - - - - - - - - - - - - - - - - - - - - -agaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtc