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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG

Basic information

species Vitis vinifera
transcript Vv01s0011g05790.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgt-tttgcagttttgtcctaaca-attgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
            | |  ||  | |   |||  ||||| | | ||      | |||    ||    ||| |   |     ||||||||||||| ||  |||||||||  |||||||| || |||||  | ||||||||||| |||||||||||||| |||||  |||| || ||||| || || || |
----------gtatctatctttatactttttaaagttgtttctgcccccctctttttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 3
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgc---agttttgtcctaacaattgt-----tttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
     | ||| |  | |   |||| | |||||  || |    ||| | ||||||     |  |||    |||||||  |         |||||||||| ||  ||||||| || |||||||| || |||||  | ||||||||||| |||||||||||||| ||| |  | || || ||||| || || ||||
-----gtatgta-tcttataatttgtgtttatctgtatccgttgtctctgttttagctgatcttttctttaacaatgataaaaacaaatgcagAATCTAGAAGTCAAGAAGATTAATGATGAGAAAAAGGCTGCAATGGCTGCTCAGTTTGCAGCAGAAGCGACTTTGCGGAGAGTACATGCAGCCCAAAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 3
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
||| || |  |  ||  | | |||    ||  |    |  | | ||| |      |||||   |  || ||   | |  | |||||| || |||   ||||| || || ||||||||||| ||  |  | || || |||||||||||||| || || ||| ||||||||||||| || |||||||
gtaatggagcagccctattcttttcctctttcacagctcatat-tgtctcgagaacagttac-tgatagcacacgatgct-gcagAACCTTGAGGCAAAGAAGATAAACGATGAAAAGAAAGCAGCACTTGCAGCCCAATTTGCAGCAGAGGCTACACTTCGAAGGGTTCATGCAGCACAGAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
gtattgcatgaaacc-cttccatttttctttataagt---tttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
||| ||| |||| || ||  ||   ||    |  |||   ||| || |  |  ||  ||   ||||     |     | ||| ||||||||||| || || |||||||| |||||||||||||| || || ||||| ||||| |||||||| |||||||||||| ||||||| |||||||| |||||||
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
gtattgcatgaaacc-cttccatttttctttataagttttgtgtgtgtgtgttttgcagt-tttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
||| ||| |||| || ||  ||   ||  | | | ||    | | |  ||    ||  || |||     |     | ||| ||||||||||| || || |||||||||||||||||||| || || || ||||| ||||| |||||||| |||||||||||| ||||||| |||||||| |||||||
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 3
gtattgcatgaaacc-cttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaa-caattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
|||||||||||| || ||  ||  |||    |  |||  | |      ||    ||   | || ||  || | | | ||| | ||||||||| || || || |||||||| ||||||||||| || || ||||| ||||| |||||||| |||||||||||||||||||| |||||||| ||||| |
gtattgcatgaagcctctatcaactttaggaaatagtcattttcccaggttaggtggtatgttttctgaatcgaatatttctggcagAATCTTGAAATTAAAAAAATCAACGATGAAAAGAAAGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTAGAAGGGTCCATGCTGCCCAGAAAG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 3
gtattgcatgaaaccct--tccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
||||| | |||| ||    || | |||  |  |||    || |    |  |   | | |  |||     |  || | ||| | ||||||||| || || || |||||||| |||||||||||||| || ||||| ||||| |||||||| |||||||||||| ||||||| || ||||| ||||| |
gtatttcttgaagcctccatcaactttagtaaatagtcattttcccaggttaggtggtatgttttctgaattaaatatttctggcagAATCTTGAAATAAAAAAAATCAACGATGAAAAGAAGGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCACGCTGCCCAGAAAG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
-----------gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
            | || |       | || |||||| |  | |   |||| | | | ||  || || | |||  |  || |   |  || |  ||||| || || ||||||||||| || || ||||| | ||| || ||||| ||||||||||| ||||||||||||||| |||||||||||||||| || ||||
gtatgtttgcaatgtttctcagttgcttttcattttccaatctc--ttttatttttctggattctgta-tttgatgatatcgcat-cttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattgcatga-aacccttccatttttcttt---ataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
||||||   || || | |||| |  |||  |    |     ||  || | |     ||  ||   | |  || |||    ||  |||||||||| || ||||||||||||||||| |||||||| || || ||||||||||| ||||| || ||||||||| | ||||| || |||||||| || ||||
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaacc--ttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
|||| || |  ||    ||| || ||||||    | ||  | | | |   || |  | | |  |  |      |||| |   ||||| || || |||||||| || ||||| ||||||||||| |||||||| ||||| ||||||||||||||  ||||| | |||||||||||||| || ||||
gtat-gcttctaatatctcctttgttctttgatcgctt-atttatattgattctata-tataatgatgttgtatgttgtc-acagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
|||| | || |||  || ||     || |||  |   |  | ||  ||  | |     || ||  |||         | ||||||||||| || |||||||| |||||||| || |||||||| |||||||||||||| ||||| || ||||| ||  | |||||||| |||||||| || ||||
gtat-gtatcaaaatctccc-----tccttacgatcatgatttggctggatatc-tgattatgaacta---------tgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG

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|122691687|gb|EC982203.1|EC982203
EST:     CAAAGGTGGAGGAGAAGCTTAAGTTAACAGAATCTCTTCTAGAAAGCAAG                         AATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCT
genomic: CAAAGGTGGAGGAGAAGCTTAAGTTAACAGAATCTCTTCTAGAAAGCAAGgtattgcatg ... ttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG
                                 tcctaac  putative branch site (score: 1)
                                          ttgtttttt  putative PPT
                                    taacaattgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC