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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagtttcatagtaatttgattgcattttgtacctatttttttgggttcttgggagaattgtttgaagatgtggattatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA

Basic information

species Vitis vinifera
transcript Vv06s0061g00810.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G08760.1 (Glycine max), 3'ss of exon 2
gtaatagtttcatagtaatttgattgcattttgtacctatttttttgggttcttgggagaattgtttgaagatgtggatt--atgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA
|||   | |   |   | |||  ||   |||     | |||  ||| ||||  | |     || |||     | | | ||   ||| ||| ||||||||||||||||||||||| || |||||||| |  |||||||| |||||||| |||
gtacacgctcggttccattttccttcgttttctctgcgattaatttaggtttattgatt--ttatttatttgtattggtttgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA

upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G19780.2 (Glycine max), 3'ss of exon 2
gtaatagtttcatagtaatttgattgcattttgtacctatttttttgggttcttgggagaattgtttgaag-atgtggatta--tgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA
|||   |    ||   | ||   | |  || | | |   |  ||| |||||  | |     || |||     || | | ||   ||| ||| ||||||||||||||||||||||| || |||||||| |  |||||||| |||||||| |||
gtacacgcacgattccatttccttcgttttctctgcgattaatttagggtttattgattttttattttctttatattgttttgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAA

upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G08890.1 (Glycine max), 3'ss of exon 1
---------gtaatagtttcatagtaatttgattgcattttgt---acctatttttttgg-gttcttgggagaattgtttgaaga-----tgtggatta------tgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA
            | | || |||  |  ||   || | || ||    || || |||||||  | |   |  | ||  |||| | |      | |  ||||      ||| ||| || |||||||| ||||||||||| ||||||||||| |  |||||||| |||||||| |||
gtaggtatacgcacaattccatt-tccttcattttctttgtgattaacttagttttttgctggtaaagaaaaaacagttttatggatttttttatattaatttgttgttcagACACGTGGTTCTGCCTCCTGAAGTTGCCAAACTGCTTCCTAAGAATCGACTTCTCTCCGAA

upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G27960.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaatagtttcatagtaatttgattgcattttgtacctatttttttgggttcttgggagaattgtttgaa--gatgtggattatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA
              ||||     ||  || | |   ||  ||  |    || |       | |  |  ||  |   | |||    |||||||| || ||||||||||||||||| || ||||| || |  |||||||| |||||||| |||
--------------gtaaagctcttcaatctcgcttcttcttcctccaattttcactctcacttctctaatcgtaatcgatcg-atacagGCACGTCGTTCTTCCTCCTGAAGTCGCTAAACTTCTTCCAAAGAATCGTCTTCTCTCCGAA

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|110397972|gb|EC964000.1|EC964000
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCGAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110392141|gb|EC957352.1|EC957352
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCGAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|71871580|gb|DT020635.1|DT020635
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|26257279|gb|CA808342.1|CA808342
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110383778|gb|EC948178.1|EC948178
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCGAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|26262419|gb|CA813482.1|CA813482
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110423493|gb|EC989839.1|EC989839
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         ACATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110401256|gb|EC967859.1|EC967859
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110423682|gb|EC990033.1|EC990033
EST:     CTGAGAAGTACTTTGATGACACCTACGAGTACAG                         ACATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: CTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|71868904|gb|DT017959.1|DT017959
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110423336|gb|EC989681.1|EC989681
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         ACATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|26257549|gb|CA808612.1|CA808612
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110414078|gb|EC979902.1|EC979902
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         ACATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
EST: gi|110396029|gb|EC961703.1|EC961703
EST:     GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAG                         GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT
genomic: GGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagttt ... ttatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctatttttttgggttcttgggagaattgtttgaagatgtggattatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA
     attttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatagtttcatagtaatttgattgcattttgtacctatttttttgggttcttgggagaattgtttgaagatgtggattatgtacagGCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG