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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG

Basic information

species Vitis vinifera
transcript Vv18s0001g00500.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
                                           | | |  ||| | |  |    | ||||| ||     |    | |    |||   | || | ||| ||    |  | |            ||| |        ||   || | | ||   | |||||||| ||||| || ||||| ||||| ||||| |||||||||||||| || || ||
-----------------------------------------cttaaatgcttttgtgaatccgtcataaggcaa----ttcatcaaaagcatttatattctgtagtttgctccctccggt------------ttaat-------caaccttggtgtcca---tacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG

upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactact-ttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
                                                        ||||  |   ||   |    |       | | ||      | |  |    ||||  |||| || |  || |||     ||||||   |||  |    || || ||     ||||||||||||| |||||||||||||| || ||||||||||||||||| ||||| ||
--------------------------------------------------------gtttcgtagatatcaaggtgatgcataaaaagtaaggcctaattatgcccttag--ttttctggttgctcttt----ctagtaatccactggtat--atgtttaa----tagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG

upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA14G39890.1 (Glycine max), 3'ss of exon 13
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
                                                             ||| |  |  | |    |    ||    | | ||  | | | |   |  || | ||    | ||  ||||| |   |||   |||||  || |  |     | |||||||| || || ||||||||||||||||| || |||||||||||||||||||||||
------------------------------------------------------------aatgttataatagacggtcc--ttaagtcattatg--tacaacga--aatctgtaattactagttagtggaagtctgaaagatctaata-tgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG

upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 13
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaa-aatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
                                                                                        | ||   | | |||   | | |   ||||   || | ||   |  | |  || |  |||     || ||||| |||||||||||||||||| ||||| || |||||||| || |||||||| || |||  ||| ||
--------------------------------------------------------------------------------------gttgctacaacttcta-actcacctcattat---cattcttgaaagatgggcaagttttaa-----attttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG

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|33402290|gb|CF207917.1|CF207917
EST:     AAAAGATTGCTGGCAGTTCTCAATATTTTCTTTTGCACCTATGTACCCAG                         GCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCAT
genomic: AAAAGATTGCTGGCAGTTCTCAATATTTTCTTTTGCACCTATGTACCCAGgtacttaatt ... caaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCAT
EST: gi|71869385|gb|DT018440.1|DT018440
EST:     AAAAGATTGCTGGCAGTTCTCAATATTTTCTTTTGCACCTATGTACCCAG                         GCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCAT
genomic: AAAAGATTGCTGGCAGTTCTCAATATTTTCTTTTGCACCTATGTACCCAGgtacttaatt ... caaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCAT
EST: gi|33402370|gb|CF207997.1|CF207997
EST:     AAAAGATTGCTGGCAGTTCTCAATATTTTCTTTTGCACCTATGTACCCAG                         GCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCAT
genomic: AAAAGATTGCTGGCAGTTCTCAATATTTTCTTTTGCACCTATGTACCCAGgtacttaatt ... caaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
                             tactaat  putative branch site (score: 1)
                  aattagtaaaatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA