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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatatttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA

Basic information

species Vitis vinifera
transcript Vv09s0002g01800.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 10
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatat-ttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA
                                                                                                 | ||  ||| |   | |     ||| ||    ||  ||   || ||||   ||   ||| | ||  | |    |  || |||||   ||  |||  ||| | || ||    ||| |  ||  |||||| ||||| ||||| ||||| || |||||||| ||| || |||||||||||||| |  |
-------------------------------------------------------------------------------------------------gtaaattttgatggccag----aatgttaggcatcattttcatattagatgataacagcctgataatgta---ttgaccttttg---ttgtctt--cagGTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G03930.2 (Glycine max), 3'ss of exon 11
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatatttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA
                                                                              | |  |      | | |||| ||     || | |||| | || | ||  ||  ||| |  ||     |  ||           || | ||   ||  | |   ||||   || |||| ||||||||||||| ||| ||||||| || || |||||||| ||||| ||||| ||||| |||||||||||||||||||| | |  
----------------------------------------------------------------------------gtaagaatgagtgatgtttttgaaa-----caaaactatacatatttttatcttgtgtaagcatgagagatgtt-----------ttttaaacaaaaactatacatatt---tttacagGTCACAGCTTCACGGCTACTATTATCAAAACAAACTATTCCTCATTACTATTTAACAGTAGATACATGTGTTGACAAACTCACGAG

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 11
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatatttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA
                                                                                   ||| || | ||| ||  |  ||   |   | | || |     || || |||  || ||  | |       |     | || | ||   |||| |       ||  || |||| |||||||||||||  |||||||||| || || ||||| || ||||| ||||| ||||| |||||||| ||||| ||||| |||  
-----------------------------------------------------------------------------------tctcct-tctgtgtgtcaatttaatgtaatgttctga-----tcttaatgt--atcttgtgtaagcatgggtgatgttttttaaacaaaactataca----tatttttacagGTCACAGCTTCACGGTTATTATTATCAAAACAAACTATCCCTCATTACTATTTAACAGTAGATACATGCGTTGATAAACTCATGAG

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatatttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA
                                                           |||| |   ||||  | || | | ||||  | ||| |||     ||||     ||  ||  | | |   | |   |  | | ||  | |    |||      ||| |||||    ||  | |||| |  ||||||| ||||||| |||||  |   ||| || ||||| |||||||| || || || ||||| ||||||||||||||||||||| | |||| 
---------------------------------------------------------gcaaatac---ctatacaaccttatatctt--gattgcttgtggtatttctagattac-ctcgaccatatatctctctgttttgtactata----agccaagaattccgaagttttgttaattgtataaatttgacagGTCACAGCCTCACGTTTGGCATTCTCAAAGCAAACTATTCCTCACTACTACTTGACCGTGGATACATGTGTTGACAAAATGATGGG

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 11
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatatttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA
                                                                                                |  || || |   |     ||    | |   | | | | ||||    |  ||  ||  ||  |   ||    || ||||||     || |  ||||||| ||||||| |||||  |   ||| || ||||| ||||| || || ||||| || || || ||||||||||||||||||||||||| 
-----------------------------------------------------------------------------------------------gtaaaacctatattactctcgcagcctttaagccagtttcaata---ggttcaacgattctgaaatctcgttcgttaacttt-----ataattttgacagGTCACAGCCTCACGTTTGGCATTCTCAAAGCAAACTATCCCTCACTATTACTTAACCGTCGATACATGTGTTGACAAACTTATGGC

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|33405959|gb|CF211586.1|CF211586
EST:     ATACAATGGCATTAGATTACACGGACCTCCCTCATTCTCAGATAAGAAAG                         ATCACAGCTTCACGTCTATTATTATCGAAGCAGACTATTCCCCATTATTAT
genomic: ATACAATGGCATTAGATTACACGGACCTCCCTCATTCTCAGATAAGAAAGgtaatactta ... accttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTAT
EST: gi|161714484|gb|FC064459.1|FC064459
EST:     ATACAATGGCATTAGATTACACGGACCTCCCTCATTCTCAGATAAGAAAG                         ATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTAT
genomic: ATACAATGGCATTAGATTACACGGACCTCCCTCATTCTCAGATAAGAAAGgtaatactta ... accttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA
                                           ttacctt  CT-rich tract
                               aacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacttattccgaactcttgttctagcatcttttggggttccaatgcatattatagaaatccattctatttagccatgtttcttctgtttgtttgcaagctttcagatctatgcttaatctttcctattgttaatatttagcacattgaagcttcatcttctgaagtcaactttttggtattaccttgacagATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA