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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA

Basic information

species Vitis vinifera
transcript Vv18s0072g00310.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 13
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctg--ttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
                                   | |  | | |    ||||    | |||  |      |||||||   | |  || |||   |    | |   |  ||||  | |       |  |||| | || |||| |||| ||||||||||||||||||| ||||||||  | ||||| ||||| ||| |||| ||  | || ||||| || |||||||| || || ||  |||
--------------------------------aagcctgatatgccaacttataaggtattcaaag-----cttttgtgcaagatgttactggccttaaaccttggcatcttagttcttaa---ctcatctgcc-ttgcagAAAATAAATGAAGATAAGCTTTTCAATCTGTTCTCTCTATATGGGAACATAGTCCGAATCAAAATACTGCGCAACAAACCAGATCACGCCCTTGTTGAAA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G052926_T02 (Zea mays), 3'ss of exon 12
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
                              ||   ||| || ||    | |  | |  |  |||   |||| |  ||   | | ||||      |||  |   ||    ||  | |    | |   | | ||  | |||| ||| ||||| |||||||||||||| ||||| ||| | ||||||||||| ||  |||| ||| | || || || || |||||||||||||| ||  | |
------------------------------ttaagctttttatttccttatggtcaggtaccct---ttatgtactgccgtgagattta-----ggccttaaaacttgctacatgtaaccattccctgt-tctgtacagAAAATTGATGAGGATAAGCTTTTCAATCTGTTTTCCTTGTATGGAAACATAGTACGAATCAAGATACTGCGTAACAAACCAGATCATGCACTTGTTGAGA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G27970.1 (Glycine max), 3'ss of exon 11
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
            ||   || || | |     |    |||| | | || | |     || |  | ||||| |    | ||||    ||       |  | || |    ||| | | |      ||||||| |  || |||||||||||||| ||||| || |||||| |||||||||| ||||| ||||||||||||||||| || ||||| ||||||||||||||||||||  ||||||
-----------gtaagtacactgcctggatat----ttctgccttttttctgaaagttctctccatttttttaaatatatttggctt-------gagttttttttttcttttttct------tttttcttt--ttccagAGAATAGATGAGGATAAACTGTTCAACTTGTTCTCCATTTATGGGAACATTGTCAGAATTAAACTTCTCCGAAATAAGCCAGATCATGCACTTATCCAAA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G08870.2 (Glycine max), 3'ss of exon 7
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
                                              |   |||      ||  |||||   | ||| |  || ||  |||| |   |  || ||  |  ||| |||||     ||   | |  || |||||||||||||| |||||  | |||||| |||||||||| ||||| ||||||||||||||||| || ||||| ||||||||||||||||||||  |||| |
---------------------------------------------gtgagtatgctgccttgatatttctgccttttttctagaaagttctctc--catttttattaaatatatttgg----cttgaatttttttccagAGAATAGATGAGGATAAAATGTTCAACTTGTTCTCCATTTATGGGAACATTGTCAGAATTAAACTTCTCCGAAATAAGCCAGATCATGCACTTATCCAGA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G36770.1 (Glycine max), 3'ss of exon 12
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
                                                        |     || | |    |||  | |  ||| ||         |||      | |||  ||     |  |||      |||||||||||| ||||| ||||| || |||||| ||||||| || ||||| |||||| | |||||||| || ||||| ||||||||||||||||||||  |||| |
-------------------------------------------------------gtaagcactgtgtctggtttcatctagaaagttctctccatttctcagcttatttagcttcaaatatgttt------atttcagAGAATTGATGAGGATAAACTATTCAACTTGTTCTCTATTTATGGGAACATTATGAGAATTAAACTTCTCCGAAATAAGCCAGATCATGCACTTATCCAGA

upper sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G30820.1 (Glycine max), 3'ss of exon 13
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
                                                      ||       | | |    ||||    || ||  |||| |    |  ||  |   ||  | ||   | || |||     |||||||||||| ||||| ||||| || |||||||||||||| || ||||| || ||||| |||||||| || ||||| ||||| ||||||||||||||  | || |
-----------------------------------------------------gtaagcactgtgtctggcttttt---ctagaacattctttccctttctcagcttatttagcttcaaatctgttt-----atttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATTGTGAGAATTAAACTTCTCCGAAATAAACCAGATCATGCACTTATTCAGA

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|351025264|gb|FQ434277.1|FQ434277
EST:     GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGAC                         AGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
genomic: GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttc ... gtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
EST: gi|110422532|gb|EC988858.1|EC988858
EST:     GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGAC                         AGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
genomic: GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttc ... gtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
EST: gi|110387338|gb|EC951996.1|EC951996
EST:     GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGAC                         AGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
genomic: GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttc ... gtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
EST: gi|349827659|gb|FQ422527.1|FQ422527
EST:     GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGAC                         AGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
genomic: GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttc ... gtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
EST: gi|351014018|gb|FQ434170.1|FQ434170
EST:     GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGAC                         AGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
genomic: GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttc ... gtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
EST: gi|349825575|gb|FQ419492.1|FQ419492
EST:     GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGAC                         AGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT
genomic: GTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttc ... gtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
                                     ctttttctgtcatttc  CT-rich tract
                        ttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA