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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT

Basic information

species Vitis vinifera
transcript Vv17s0000g01540.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttcccttttta-gcataat-ctgaattttatttgt----gtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
                                                       | |||    | ||    | | | |  || | || || |           ||| | | || | | ||| | | ||   | | | ||||       ||| |  |||||||| ||||| ||||| ||| | ||||| ||||||||||| ||||||||||||||||  ||  | || ||||| ||  | |   |||| ||||||||  |
gtatgccatcctgcattatactataccatttttatgcaatgaataatacaattattcattttattttattctcatctgtagctgtaaattaagaccaaatcatcactattcattataatgcaaagtgctacttctaacttgtcaacacctttttattcagCTGGGAAGTCCTCAGTGTTGCTTGATGTCAAACCATGGGACGATGAGACTGACATGACCAAATTGGAAGAAGCTGTGAGGAATGTTAAGATGGAAGGCCT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G031545_T03 (Zea mays), 3'ss of exon 5
---------------------------------------------attattgagatgtacctgcctatatttcttttaaa---tatgggtc-ctctcctacttt------ccctttttagcat-----aatctg-aattttatttgtgtgttt-------attctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
                                               | |||| |||| |   |    || | |  | |      |||  | || |     |||      | || |||   ||     ||  ||  |||| ||   | |  ||       ||| |||||||| ||||| ||||||||  | |||||||| |||||||| |||||||||||||||   ||||| |||||||| ||  | ||  |  | ||||||||| |
gtatgtcagtgtgcatattttttctgtttcattctctcatcacactgtgttgacatgtgctgacactaatctataatgacacccttggaccactatatcgttttttgaagctctgtttgatatccaaaaacttgtgatttcatcaatcttctttccatacattgtcagCTGGGAAGTCATCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGGCT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G153569_T02 (Zea mays), 3'ss of exon 5
---------------------------------attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
                                  | | | | |    | ||| |||   | | ||     || | | |    |  |  ||         | |   ||  | | |  | |   |   || |||||||| || || ||||||||  | |||||||| |||||||| |||||||||||||||   ||||| |||||||| ||  | ||  |  | ||||||||  |
gtatgtcagtgtgcatagtttctgttttattctctcaatcacacacccttgc-tattgctatattgttgttgaggctttgtttcatacccaaaagctttaaagcatggttctaacctttccataccttgtcagCTGGGAAATCGTCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGACT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G07350.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------attattgagatgtacctgcctatatttcttttaaa-----tatgggtcctctcctactt-----tccctttttagcataatctgaattttatttgtgtgtttattctca---gCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
                                                                                ||  |||  || |||     | ||||   ||| ||     ||  |  |||| |||   |     | ||  |||   |     |  ||||| |   ||  |  |||||||   ||||| ||||| || ||| |||||||||||||||| ||||||||||| ||||||||||| ||||| |||||||||||| |    ||| | |||||||||||
gtattttcccaatgataaaatgtggttgattaatttcttgtttccttttcacattatgtgccttaactcatggttggttcatctttgtcatttactcat-tgtattgtctttgaactttatactgcccctcccctgactatacataccactttgtgagggcattgattttgtgc-tgattccattctcaacagCTGGAAAGTCATCTGTTATGTTGGATGTGAAACCTTGGGATGATGAAACTGACATGAAGAAGCTCGAGGAAGCAGTAAGATCTATTGAGATGGAAGGGTT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
----attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
     ||  |    |||  ||   ||| |||    |  ||   |  |   ||    | | ||  |||   ||    |  ||| | | | ||  |   || |||||||| || || || ||| |||||||||||||||||||||| ||||| ||||||||||| ||||| || ||||||||  |     || | |||||||||||
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgt-tgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G37120.2 (Glycine max), 3'ss of exon 5
----attattgagatgtacctgcctatatttct-tttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
     ||  |    |||  ||   ||| |||    || |   |    ||||  | | | | ||  |||   ||    |  ||||| |   ||  |   || |||||||| || || || ||| |||||||||| ||||||||||||||||| ||||||||||| |||||||| ||| ||||  |     || | |||||||||||
gtgagtttctttcttgtcactagttatctttgaactttatcctaccccctcctccattataccactttgtgatggcattgattttctgc-tgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTAAAACCATGGGATGATGAAACTGACATGAAGAAGCTTGAAGAATCAGTGAGATCTGTTCAGATGGAAGGGTT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
 | | |  |  ||      |||   || |  |  |||||  |  | |     | ||     || |  |  ||   ||| | ||| | | ||  |  | |||||| ||||| ||||||||| | ||| | ||||| ||||||||||||||||||||||| |||||||||||||| ||      |||| | |||||||| ||
gtaagtttgg-gttttgttctacccttgtaatttatatgaatgatatgaagatgtc-----ttggatttctc---attgtttttat-tattcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G18110.1 (Arabidopsis thaliana), 3'ss of exon 4
attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattc--tcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
          |     ||  | | || | |||| |  ||     |    ||   |    | || |  |  ||   || |  ||| | | |||  |   ||||| || ||||| ||||||||| ||||| | || || |||||||||||||| |||||||| ||||| |||||||| ||| |   |||| | |||||||| ||
---------gtaagtttgtgttt-ttgcctttacacctgtagtttacgatataatgatgtcttggatttctc---atctggtttctttcttttcttaatcagCCGGAAAGTCATCAGTTTTGATGGATATCAAGCCGTGGGATGATGAGACGGACATGAAGAAGCTAGAGGAAGCTGTAAGATCCATTCAGATGGAAGGATT

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|30125273|gb|CB910612.1|CB910612
EST:     TGCTGAAGCACGAGCAGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAGT                         CTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTG
genomic: TGCTGAAGCACGAGCGGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAGTgtgagtatct ... ttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTG
EST: gi|110703308|gb|EE080039.1|EE080039
EST:     TGCTGAAGCACGAGCAGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAGT                         CTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTG
genomic: TGCTGAAGCACGAGCGGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAGTgtgagtatct ... ttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTG
EST: gi|110701720|gb|EE079612.1|EE079612
EST:     TGCTGAAGCACGAGCAGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAGT                         CTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTG
genomic: TGCTGAAGCACGAGCGGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAGTgtgagtatct ... ttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
                                            tttattctc  CT-rich tract
                             aattttatttgtgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - -acctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt