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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA

Basic information

species Vitis vinifera
transcript Vv09s0002g00100.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 13
--gttttttttttccacgtcaagttattgcct--tttgattttcgtttatttagtact--attatagcatattgtaataattttaagctattggattca--acttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA
  |      |||| || |         |  ||  | |    |  ||   | || || |    |  |   |  | | |   |  |    | |  |  |||    | ||||||||||||||| ||| ||||  | |||||||||||||| ||  | |||||||| || || || || || ||| ||||||| ||||||||||| || |||
gtgaggacattttgcaagagcgccccctatctgatatatcataggtaggtctaatagttggatgcacacttctctcacgttcctttcttttctgtctcactgttacagATCTGTTTACAAGACTATCCCGGACTGTGAACCTTGCCGACCTCTGCAAAGATCACCGATTGAAGGGTTCTATCTAGCTGGTGACTACACAAAGCAGAAA

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
--gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattc-aactt-------cagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA
  |    | ||| |       | ||  || |   | |   |   |   |     || | |||   |  |||  |  |||  |    ||| ||||   |||       |||||| |||||||||||||||||||| ||||| |||||||| ||  | ||||| || ||||| || || || ||| ||||||| || |||||||| || |||
gtgaggatatttgctgaagacacttcctgacagataaccataagtagctcta-gctctgataattttatgtgttgttttctaatgtttgtattctggcttgctttgacagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 12
------------gttttttttttccacgtcaagttattgccttttgattttcgtt--tatttagtactattatagcatattgtaat---aattttaa----gctattggattca--acttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA
                  | |  | | |||   || |||    |  | |   | |   |||||   |  ||| |      |||  |   |||  |||     ||| ||| | ||    ||||| || |||||||||||||| ||||||||||||||||| ||||||||||||||||||||| |||| || || ||||||||||| || |||||||||||||||
gtttgattgaataaccagtctggcaatgtct--ttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAGATCTCCTTTAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
----------------------------------------gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattca--acttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA
                                        | || |||| |  |  |  | ||      | ||  || |   |||  || || |   ||    | || | | |   | | |  | ||  | ||    ||||| || |||||||||||||| ||||||||||||||||| || ||| | ||||||||||||||||| || || ||||||||||| || |||||||||||||||
gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatt-tgtgttctga-atcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA
  ||  |          ||  |  ||  |||   ||    |   |    |   ||   |   | |||  || |  |||   ||||||  | ||   |||||||||| ||||| ||  ||||||| |||||||| || |||||  |||||||||| ||||| || || || || |||||||| || ||||||||||| || 
-gttagtgaagttgtaccatttatttagcttcaaatgagggacca---ggctttacattgataaatt-caacatctttct-ctattgt-tgcatgatcagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG

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|45771660|gb|CN007512.1|CN007512
EST:     GATCAGAGCAAAGCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAG                         ATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAG
genomic: GATCAGAGCAAAGCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAGgttagaatga ... tcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAG
EST: gi|352778350|gb|FQ465660.1|FQ465660
EST:     ATCAGAGCAAAGGCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAG                         ATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAG
genomic: ATCAGAGCAAA-GCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAGgttagaatga ... tcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAG
EST: gi|110392879|gb|EC957437.1|EC957437
EST:     GATCAGAGCAAAGCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAG                         ATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAG
genomic: GATCAGAGCAAAGCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAGgttagaatga ... tcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtactattatagcatattgtaataattttaagctattggattcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA
     tactattatagcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattcaacttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA

- - - - - -ccacgtc
- - - - - - - - - - - - -tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctattgg