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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT

Basic information

species Vitis vinifera
transcript Vv07s0191g00060.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                                  |   |    | |  ||   || |    ||  | || | |  |   |||| |   || |       ||      |||  ||  ||||||| |||||||||||||| ||||| || ||| |||| ||||| ||||||||| |||| ||||| ||||| || ||||||||||| || ||| | |||||
-------------------------------------------------------------------------------------------------gtaaaaaggctctatttctattattgactttcggatattcatgcc-cttgctctgaccatattatgtta----cttgtatgg-cagGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 4
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaat-tggcattttgct-tgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                    | |   |||     || |  ||||    |   | ||| ||||| ||| |||||| |     || |    |||||  |||| |  ||||||  |    ||||| ||||| ||||||||||||||||| || ||| |||| ||||| || |||||| | || ||||| |||||||| ||||| || ||||| ||| | |||||
-----------------------------------------------------------------------------------gtagatgtttaaga-tgcttacatttgaatggttatgtttcattttgc-tttgct-ggcaggtgtt----ctaatgtgaatgttccatttttatactgacagGTACCCCCTGCTTCCGTGGATATGGCAGGCGTGATGGTGAGCGCAGAAGGAAGTCAGTCCGTGGTTGCATTGTCAGCCAAGATCTCTCTGTTATCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G054136_T06 (Zea mays), 3'ss of exon 3
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                 |  || |    ||    | | |  | ||   ||| |   || |||  |   |      |||  |  | |     ||| |||     |||  || |||       | |   ||    |||||| || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||| ||||| || ||| | |||||
-----------------------------------------------------------------ttctgctccataggg-gtatagagactt---cctatgtccagtgtactc--tcaacaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                  | | |  | ||   ||| |   || |||  |   |      |||  |  | |     ||| |||     |||  || |||       | |   ||    |||||| || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||| ||||| || ||| | |||||
---------------------------------------------------------------------------------gtatagagactt---cctatgtccagtgtactc--tcaacaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                  | | |  | ||   ||| ||  || |||  |   |  |   |||  |  | |     ||| |||     |||  || |||       | |   ||    ||| || || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||| ||||| || ||| | |||||
---------------------------------------------------------------------------------gtatagagactt---cctatttacagtgtactc--tcagcaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                               | || |   | || || ||    |  | ||   ||| |   || |||  |   |  |   |||  |  | |     ||| |||     |||  || |||       | |   ||    |||||| || ||||||||||| ||||| || |||||||  ||||| ||||||||  |||| ||||| ||||| || ||||| ||||| || ||| | |||||
--------------------------------------------------------------ctctactccataggggtata----gagactt---cctatgtccagtgtactc--tcagcaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 4
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgt-tagcattgtggttaatttgtctcat-tctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                   ||    |||||     || ||      | |||  | | ||   | ||| ||||| ||   |  |  |  ||   | |     ||    | || |||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| ||| |||||||||| |||||||| ||||  |||||||| |||||||||||
-----------------------------------------------------------------------------------ttattaatttttaatagtgtaatgcatttgttgttatatcaggtgtctacattttctt--ttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgat---gaaactaatacgaattggcatt-ttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                          | |||   | |||  | |||  |  ||||||   ||   |  | |   |  | |||  |    ||||||||     ||    || || |||||||||| || ||||||||||||||||||||||| ||||||||||| || ||||| ||| |||||||||| |||||||| ||||  |||||||| |||||||||||
---------------------------------------------------------------------------------------ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 4
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                |||      |  ||   || | |  |  |      |||| |   |   |    | ||   ||||||| |   | |  |   |||     ||    |||| |||| || ||||| ||||||||||||||||| || ||||||||||| || |||||  |||||||||| |||||||| ||||  |||||||| |||||||||||
-------------------------------------------------------------------------------atatgcaatgacctttagctttcacta--gaaacctatttatgcaagattctcatagcc--atgcttgtttgcagtcttgttaatcttttttgcatttgagcagGAACTCCTTGTTTCCGTGGATATGGAAGGCGCAATGGAGAGCGTAGAAGGAAATCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 4
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttg-tctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                                  ||  || | | | |  | |||  | ||   | |      | | |  |  | |||| |   |  |  |||    |||     ||| |    || |     |||| || ||||| |||||||| |||||||| || ||||||||||| ||||||||| |||||||||| |||||||| ||||  |||||||| ||| | |||||
---------------------------------------------------------------------------------tttgaggtactgtttttttttataactggactcaggaaacttttagccaacctttgttattttttcaatg---ttaaatttcatttgttgcttacccatgcagGAACTCCTTGTTTCCGTGGTTATGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 3
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattg-ttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                           |||||  | || ||||    ||||  | |  |  || || |   || ||| |     ||  || |  ||    | ||| |  ||| ||                 || ||||||     || |||| || ||||| ||||||||||||||||| || ||||||||||| || |||||| |||||||||| |||||||| || |  || ||||| ||||||||| |
-----------------------------------------------------------tttatgcaatgatttttagctttaactagaaaccttttcattgcaggattctcagccat--gtttatttgcagacttgtt-aatgttt-----------------tttgcattt-----gagcagGAACTCCTTGTTTCCGTGGATATGGAAGGCGCAATGGAGAGCGTAGAAGGAAGTCTGTTCGTGGTTGCATTGTCAGTCCAGATCTCTCTGTTTTGAACCT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 5
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                            |||    |   | || ||    | ||||    ||   |  ||| ||  |  |    | || |    |    |||  |  |||     || |    || | ||| |||| || ||||| |||||||| || ||||| || ||||||||||| ||||||||| |||||||||| |||||||| ||||  |||||||| ||| | |||||
----------------------------------------------------------------------------agtaaggtcatgtatatttgttttttag----gta-ctgctttttcataaccaatttatgttattggtccaatgtta--aatttctgtttgttgcttacctgagcagGAACTCCTTGTTTCCGTGGTTACGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 2
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                                                                       |||   |   ||  |    | |  |  || ||  | |    ||| |   | | |   ||   |||   |||  ||  | ||     |  | ||||     |||  | |||||| || ||||||||||||||||| ||||| || || |||||||||||||||||   |||||| || |||||||| ||||  || ||||| ||| ||||| |
-----------------------------------------------------------------------tttatggcagat--gcatgtctctttatgctatgact----ttattccttttgaagatggtcttgagggatattt--ttaattctctttgcattga----ttgtgttaacagGAACTCCTTGCTTCCGTGGATACGGAAGGCGCAACGGAGAGCGAAGGAGGAAATTTGTTCGCGGGTGCATTGTCAGCCCAGATCTCTCTGTTCTGAACCT

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|349825698|gb|FQ421797.1|FQ421797
EST:     GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAG                         GCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
genomic: GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAGgttggtagac ... gcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
EST: gi|110406936|gb|EC972523.1|EC972523
EST:     GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAG                         GCACCCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGAAGGAGGA
genomic: GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAGgttggtagac ... gcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
EST: gi|351027768|gb|FQ446935.1|FQ446935
EST:     GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAG                         GCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
genomic: GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAGgttggtagac ... gcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
EST: gi|32269925|gb|CD719084.1|CD719084
EST:     GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAG                         GCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
genomic: GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAGgttggtagac ... gcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA
EST: gi|110732898|gb|EE108585.1|EE108585
EST:     GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAG                         GCACCCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGAAGGAGGA
genomic: GAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAGgttggtagac ... gcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
                       aactaat  putative branch site (score: 2)
                                         ttttgctt  putative PPT
                      aaactaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT