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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctccttgatttaatttgctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA

Basic information

species Vitis vinifera
transcript Vv17s0000g08170.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 10
--------------gtatctccttgatttaatttgctgttacatatagatcaactctatgg-------agttctgaagtat-tgttttcttttaa--cagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA
                | || | ||   | |     |||| |    | | ||  || |||        |        |||| |||    ||| ||  ||||||||||||||||| |||||||||||  | || ||||| || ||  ||||||| || |||||||||||| | ||||| ||||| || || || || || |
gaattacatggagcccaactacctgtaatgaacacttgtttccctcaaagcatgtcgatgtttaggctaacataatggtatgtgtacattttcaatgcagGATGCCATGTCTGTTGCAAGAAACATTTTGAAAAATCCGAAACTCCTTCCTGGAGGTGGTGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 10
gtatctccttgatttaatttgctgttacatatagatc-aactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA
|||     |||   |  | |   |    || ||| ||  |   ||  |  ||||||    || |||||||   |||||||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || |||||||||||||| || || |||||| || | |||||||| |
gtaagctattggcatggtctaaag----atttagttctgatcatactgctttctgagaacttattttctt--gacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCAAAACTTGTTCCTGGAGGTGGTGCTACAGAGTTGACAGTGTCAGCTGCCTTGAAACAGAAGA

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 10
gtatctccttgatttaatttgctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA
|||     | ||  |  | |     |  |  |   |  ||  ||  |  |||||||   ||||||||||   |||||||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| || |||||||||||||| || || || ||| || | ||||| || |
gtaagctatcgacatgttctaaaaatttagtt---ttgaccatactgctttctgaaac-ttgttttctt--gacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 7
gtatctccttgatttaatttgctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA
|||     |||||||   |  |     | | | |||    || || |  |||||||||    |||||   | |||||||||||||||||| ||||| ||||| ||||| ||| |||| ||||||||||| || |||||||| ||||| ||| | ||||| || || || ||||| |
gtaaagtgttgattt--ctacccagagcttgtggatttgatc-attgctttctgaagt----ttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA

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|110365989|gb|EC929587.1|EC929587
EST:     TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAG                         GATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCT
genomic: TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAGgtatctcctt ... cttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCT
EST: gi|161716671|gb|FC065567.1|FC065567
EST:     TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAG                         GATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCT
genomic: TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAGgtatctcctt ... cttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCT
EST: gi|110392915|gb|EC957538.1|EC957538
EST:     TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAG                         GATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCT
genomic: TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAGgtatctcctt ... cttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCT
EST: gi|294966380|gb|GW839487.1|GW839487
EST:     TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAG                         GATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCC
genomic: TTAGAGGTGCGAGCAAGGATCTTTTGAATGAAGTGGAAAGAAACTTGCAGgtatctcctt ... cttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA
                                    tattgttttctttt  CT-rich tract
                                    tattgttttcttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctccttgatttaatttgctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT