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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagaaagatataaatgcagctattcaggtttgatggattattcaaacatgcccttggtgaatacttgacaagatctctcattcttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG

Basic information

species Vitis vinifera
transcript Vv15s0046g02460.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 9
atagaaagatataaatgcagctattcaggtttgatggattattcaaacatgcccttgg---tgaatacttg-acaagatctctcattcttgtt--gatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
                | |  ||||  |   || ||  |      | |||    | ||   ||   ||||  | || |  |||   |||| ||     || | ||||| ||| ||||||||||||||||| | ||||| || |||||||||||||||||| | || ||   ||||||  ||||||||||||||||||||
----------------gtaattattgtgccctgctgcttatgcttaccatatagtggggagtggggacttttataacaattcttgctctttttccatcatgatcagGTCGGATCTGTTCTTCTCAGTTGTTCCTTCTTATATGACATCTTTTGGGTTTTTATCTCCAAGATGTGGTTTCATGAGAGTGTGATGATTGTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------atagaaag-------atataaatgcagctattcaggtttgatggattattcaaacatgcccttggtgaatacttgacaagatct-ctcattc-ttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
                                                                                      ||| |  |       |||| | || | |  || |   | |||  | | |  |    || ||||  | | ||    | || |     | || | || ||   ||  | |||||||||||||||||||||||||||| ||| | ||||||||||| ||||| ||||| ||||||||||||||| |||||||||||||||| |||
gtgattatacattacttaagcttgtattttgcacaatcacctacttaggttgtttgttatattcttgaaaattaagcttgggatgcataaaggggacctccatatcagtgaaacatttaaatatggatctactgtctattactgaccttttttattaacaaaaaacactaatttatacattttttccatgta-agGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 9
atagaaagatataaatgcagctattcaggtttgatggattattcaaacatgcccttggtgaatacttgacaagatct-ctcattc-ttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
 |    | || | | || | | ||| |   | |||  |   |  |    || || |  | | ||    | ||||     | || | || ||   ||  | |||| ||||||||||||||||||||||| ||| | ||||||||||| ||||| ||||| ||||||||||||||| |||||||||||||||| |||
-tttttatatttcagtgaaacgattaaatatggatctacagtgtattactgaccatttttattaacaaaaaagactaatttatacattttttccatgta-agGTCGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G01100.1 (Glycine max), 3'ss of exon 9
-atagaaagatataaatgcagctattcaggtt--tgatggattattcaaacatgcccttg-gtgaatacttgacaagatctctcattcttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
 | | |    |  | |   |||| | | || |  |  || | | ||   |    |      |     |||   | | || |  | || ||  |||    | ||||||||||||||||||||||||||||| ||| | || ||||| |||||||| ||||| |||||| |||||||| |||||||||||||||| |||
gacaaatcattgaagacatagctttgctggatactactgaacttttattatgaacaaaaaagcacccactgaccgacatatacctttttttctga----atcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 10
---atagaaagatataaatgcagctattcaggtt--tgatggattattcaaacatgcccttggtgaatacttgacaagatctctcattcttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
   | |||  | |  | |   |||| | | || |  |  || | | ||   |    |          ||||     | || |  |||| |   |||    | ||||||||||||||||||||||||||||| ||| | || |||||||| ||||| ||||| |||||| |||||||| |||||||||||||||| |||
ctgacagatcgttgaagagatagctttgctggatactactgaacttttattatgaacaaa-aacacctactgactgacatataccattttctctga----atcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATCTTCTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G01100.2 (Glycine max), 3'ss of exon 9
-atagaaagatataaatgcagctattcaggtt--tgatggattattcaaacatgcccttg-gtgaatacttgacaagatctctcattcttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
 | | |    |  | |   |||| | | || |  |  || | | ||   |    |      |     |||   | | || |  | || ||  |||    | ||||||||||||||||||||||||||||| ||| | || ||||| |||||||| ||||| |||||| ||||                         
gacaaatcattgaagacatagctttgctggatactactgaacttttattatgaacaaaaaagcacccactgaccgacatatacctttttttctga----atcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTG-------------------------

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 9
----atagaaagatataaatgcagctattcaggtttgatggattattcaaacatgcccttggtga--atacttgacaagatctctcattcttgt-tgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
     ||||  |||| ||      ||    | || |    ||  | ||        |  |  | |  ||| | |  | |||  ||||||    | | |  ||||||||| ||   |||||||||||| ||||| ||| |||| |||||||| |||||||||||||| ||||||||||||  ||| || ||||||||||||
gctggtagacggatacaatcatttctgccaatgtatagaagaccaatc-------tctataataacaatattagttatgatgactcattgaactcttacgtaaacagGTCGGGTTTGTTCTTCTCAGCTGTGCCTTCATGTATGACATCTTCTGGGTTTTTGTTTCAAAATGGTGGTTCCGTGAAAGCGTGATGATTGTG

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|110401255|gb|EC967858.1|EC967858
EST:     TTGCACTCATCATCACAGTTCTTCAGATCGTTCGTGTTCCTAATCTCAAG                         GTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTT
genomic: TTGCACTCATCATCACAGTTCTTCAGATCGTTCGTGTTCCTAATCTCAAGgtgattgcat ... atataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTT
EST: gi|110369217|gb|EC933370.1|EC933370
EST:     TTGCACTCATCATCACAGTTCTTCAGATCGTTCGTGTTCCTAATCTCAAG                         GTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTT
genomic: TTGCACTCATCATCACAGTTCTTCAGATCGTTCGTGTTCCTAATCTCAAGgtgattgcat ... atataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgcccttggtgaatacttgacaagatctctcattcttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG
                                        tgttgat  putative branch site (score: 4)
                                          ttgatataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagaaagatataaatgcagctattcaggtttgatggattattcaaacatgcccttggtgaatacttgacaagatctctcattcttgttgatataaacagGTTGGAACTGTTCTTCTCAGTTGTGCGTTCTTGTACGACATCTTTTGGGTTTTTGTTTCTAAATGGTGGTTCAATGAGAGTGTGATGATTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- agaaaga
- - - - - - -aatgcag
- - - - - - - - - - ctattca
- - - - - - - - - - - - - - - -tgatgga
- - - - - - - - - - - - - - - - - - - - - - - -catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaga