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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA

Basic information

species Vitis vinifera
transcript Vv03s0038g04500.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagt--ataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctc-ttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA
                                        ||| |||||    |  |  ||| | ||    ||    |     |||  |    ||     || |   |   | | | |||     | | |  |  ||||    ||||  || |||||||||||||| || ||| |||||||  | || |||||||||||||||||||||||| | |||||||| ||||||||||| ||||| ||||| ||||| |
---------------------------------------gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G01280.3 (Glycine max), 3'ss of exon 10
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA
                                                               |   | |  |||||  ||||  | |   ||  | ||||     || ||| | |||||      | || || |   | |||| | |||||| ||||||||| |||||| |||||||  | || |||||||||||||| ||||||||| | |||||||| ||||||||||| ||||| || || |||||  
--------------------------------------------------------------gtatgtgtaatgtttagcacttctttaagtttatcttttga---ctcttttacttgttt-----accccctaat--gtacttcattgcagACTTTGAAGATAAATCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA
                                        ||| |||||    | |||    ||| ||        ||| ||    || |   |  || | |  |  |||  |      | | || |     || |    | ||  ||  ||||||||||||| || ||| |||||||  | || ||||||||||||||  |||||||| | |||||||| |||| |||||| ||||| ||||| ||||| |
---------------------------------------gtatgtgtaaatgttttaaggattttatttgc-----tttaacgtagatgcccacagatatataccattatgcg------ttcgtataaa---ttgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA
                                                               |   | |  |||||  ||||  | ||  ||  | ||||     || ||| | |||||      | || || |    |   ||   ||||| |||| |||| |||||| | |||||  | || |||||||||||||| ||||||||| | |||||||| ||||||||||| ||||| || || |||||  
--------------------------------------------------------------gtatgtgtaatgtttaacacttcttttactttatcttttgg---ctcttttacttgttg-----accccctaatctacttctt---gcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 11
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA
                   | |||   |   ||||    | |||||       |  |||    || ||   || |  |  |  | || |||  |  ||  |||| |  |  |   |  ||  ||  ||| |     | | |  ||  | ||| |||||||||| |||||| |||||||  | || ||||||||||| || | ||| ||  | ||||| || |||||||||||  |||||||||| |||||||
------------------gtgagtataaa--caaacacatgatttgctgattcttcaatc---ttgtttgagtttgatgaatgcataatctacca-ataattctttgcaactatatgctt--atttatctt-----tgggatatt--tacagGTTTTGAAGATAAATCCAGAGAAGAAAGATATAGATTCTTTTGTTGCGGATGACTTTGAGCTCATTGGCTATGATCCTCACAAGAAAATAGATATGAAAA

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|33405951|gb|CF211578.1|CF211578
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|352776732|gb|FQ472619.1|FQ472619
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|33401638|gb|CF207265.1|CF207265
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|45770374|gb|CN006226.1|CN006226
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|110361466|gb|EC924940.1|EC924940
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|110381698|gb|EC935151.1|EC935151
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|33407075|gb|CF212702.1|CF212702
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAACCCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGACCATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
EST: gi|110413975|gb|EC979795.1|EC979795
EST:     ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCA                         ATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT
genomic: ATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCTTTTCCAgttagtattc ... tttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA
                                           actttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG