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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
                 |    ||  | | || |  | |    || ||    | |   ||| |  || |    || |||  | | ||     | | |  ||||||||| ||||| ||||||||||| ||||||||||| || |||||||  ||||||||||||||||| 
-----------------gtcagttggcctgtttgcaa-acagaatcgatcaatcaaacagagaagctga----tctcatgccctactatgttttcttattcagGTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGTGATCTTTACCCACAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttcttt-cttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
                   || |  |||   || | | |||      || |||  || | |  | ||||    |||  |||| |  | ||   |   || |||| || | ||||| ||  | || || || ||||| |||||||| ||||||||||||||||| ||||||
----------------gttttctgttcaccatgctaatatgttg--aaaactt--gtaatactttcttatacgtcatgtttcctaacctgttctatttt-tcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacattt-ctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
              |   ||| |||  |   || | | |||      || |||   |   |  | ||||    ||   ||| ||  | ||       || |||| || | ||||| ||  | || || |||| ||| |||||||| ||||||||||||||||| ||||||
-------------gttttcttgttc--accatgctaatatgttg--aaaacttgtat---actttcttatacgtcttgtttactaacctgttccatttt-tcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
                |  ||  |||  |||  |   |||   ||  ||   ||| | || || |  |  |  | ||| || ||| ||  ||       |||||  || |||||||||||||| || |||||||| || |||||||||| ||||||| | |||||||| 
--------------gtaagttggtct-gtttcag---catagaataaaa---taatttagcaagcactt-gtctaacagtttttttttttcaaa-----tcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagctt-aagtgagaaatccttaaggttcacatttctttct-----tgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
         |    ||   |  |  |  |||||| |  || |  |   |||   |||||  || | ||     ||   | |    | |     | | |||| |||| ||||| |||| |||||||| || ||||| |||||||||||||| || ||||||||||| ||||| |||
------gtatgggctctattattcatttttttggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgagatgtgtaagtactatgc-ttcttagGTTGCTGACGGAGAAAGGTTACCTTTAGCTGTTAAGGAGTTGGGCACCTGTGATCTCTACCCCCAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatc-cttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
         |    |||  || | | | |||||      | | ||  ||||  |||||  || |  ||| ||   |||||     | ||   |||  || | || || ||||||||||||| || || ||||||||||||||||| || ||||||||||| || || |||
------gtatgggctcatttt-taccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgcaagtatt---atgtttttt-agATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagctt-aagtgagaaatccttaaggttcacatttctttct-----tgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
|| ||  ||    |    ||| || |  ||| || |  || |  |   |||   |||||  || | ||     ||   | |    | |     | | |||| |||| ||||| |||| |||||||| || ||||| |||||||||||||| || ||||| ||||| ||||| |||
gtatgggctctgttattcctttttttt-tttgggctgtataatttgcgagcaagaagtgttaagttctctttatttttagtgacatgtgcaagtactatgc-ttcttagGTTGCTGACGGAGAAAGGTTACCTTTAGCTGTTAAGGAGTTGGGTACCTGCGATCTCTACCCTCAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatc-cttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
         |    |||  ||   ||  ||||       | | ||  ||||  |||||  || |  ||| ||   |||||     |    | |||  || | || || |||||||||||||  | || ||||||||||||||||| || ||||||||||| || ||||||
------gtatgggctcatttttacctttttttatccgtctaatatgtaagcaaaagtggaaacttgctttagtgacacatgcaagt---actatgtttttt-agATTGCTGATGGAGAAAGGCTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCACAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 10
gtttgaacttaaattcagcttattc-tcattttggttacatgacattgaa--gcttaagtgagaaat-ccttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
            |  |  | || |  | | | |  |    || ||| | |   | ||  ||     |   ||  |  | |   |   || |||   ||    || ||||||||||||||||||| ||||| |||  |||||| ||||| || |||||||||||||| ||||||
----------gtacacgccatacttgtaactcttatactgtggcataggatgacctatttgttttttgtttttcgcctgatgataagtttttgttctgtaa-cttagGTTACTGATGGAGAAAGGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 10
gtttgaacttaaattcagcttattctcattttgg--ttacatgacat-tgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgcct---tctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
|| |       ||||     | || | ||| |||  |   |  || |  |   || |  |    | |  |   |  | |   || |    |  |||  ||    || ||| |||||||||||||||| | || ||| ||||||| ||||| || |||||||||||||| ||||||
gtctagctcctaattgtaactcttgt-attctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaagctttcatctctctaccttagGCTACTGATGGAGAAAGACTTCCCTTGTCTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA

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|351030017|gb|FQ430759.1|FQ430759
EST:     TAAAGAGTGTGGGAGCGGATTTTGAG                         GTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGT
genomic: TAAAGAGTGTGGGAGCAGATTTTGAGgtttgaactt ... gccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA
                              tttctttcttgccatg  CT-rich tract
                             atttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG