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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttggtatctgatttctttacaatggatactttgatctctcagacatgggtattgaagtgaaaacatgaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG

Basic information

species Vitis vinifera
transcript Vv17s0000g01540.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G37120.2 (Glycine max), 3'ss of exon 2
gtaagttttggtatctgatttctttacaatggatactttgatctctcagacatgggtattgaagtgaaaacatgaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG
        ||||   | ||        | | | | || | | ||   |    |   | ||    |  |||             |  ||  ||| |||  |   |||  | |||      |  | | |||||||||||| ||||||||||| | |||||| |||||||| |  |||  |||||||||  |||||| |  ||||| || ||||||||||| ||||| || 
--------tggtggtttatgct-----agtaggttctgtcaactactatttttttttctttcttttcaaatcctt--------tatttcttacgtatcgtcccttt--tgaat-----gtgcttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGCTCCATCAGATGAATATGGAAATGTTTCCAGGTGGTACAAGCACATTGAT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 2
gtaagttttggtatctgatttctttacaatggatactttgatctctcagacatgggtattgaagtgaaaacatgaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG
               || ||| | |     || ||  |  |  |||   |  |   | ||    |  |||             |  ||  ||  |||| |   |||   |  |      | || | |||||||||||| ||||||||||| | |||||| |||||||| |  |||  |||||||||  |||||| |  ||||| || ||||||||||| ||||| || 
-------------ggtggtttatattggtaggttatatcaacttctattattttttttttccttttcaaatcct---------tatttcttatgtattgtcccttttgcattt------tctttttagGTACCAAGCTACAAAGGATGATCTTACTGTTTATGCAGCTTTGCCAACTGCTCCATCAGATGAATATGGAAATGTTTCCAGGTGGTACAAGCACATTGAT

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G07350.1 (Glycine max), 3'ss of exon 1
gtaagttttggtatctgatttctttacaatggatactttgatctctcagacatgggtattgaagtgaaaacatgaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG
                                     |  || || |   | |   | ||    |  ||   |          || ||  ||  |||| |     | |     |||   |||| | |||||||||||||||||||||||| |||||||| || ||||  |  |||  |||||||||  ||||||                                  
------------------------------------gtatatgtcactagcttcttttttttttttgaattct----------tgtttcttatgtattgtctccctttg----catgtgtttttttagGTACCAAGCTTCAAAGGATGATCTCACTGTT-ATTCAGCATTGCCAACTGCTCCATCACATGAATAT---------------------------------

upper sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G18110.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagttttggtatctgatttctttacaatggatactttgatctctcagacatgggtattgaagtgaaaacatgaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG
       || | ||||| |||||    || || |         |||||   ||   | |||   |||||  ||       || | |  | ||| |  |    | |   ||  | ||  || ||   ||||||||||||||||||||||||||||||||   | |||||||||||||| | ||| | || || |  || ||||| ||| | |||| ||||||||| || 
------gttagaatctgttttct----aagggctg--------tctcaattatctatcttgttttgaaacaatag-----tagtaaccattactttcttctgtctctctatgt-atgtatgtttatagGTACCAAGCTTCAAAGGATGATATCACTGTGTTTACAGCTCTTTCAAAGCCCCCAACTTCAGAGTTTGTCAATGTATCTCGTTGGTTCAACCACATCGAT

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|71867690|gb|DT016745.1|DT016745
EST:     GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGTGG                         GTACCAAGCCTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
genomic: GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGTGGgtaagttttg ... attttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
EST: gi|110703308|gb|EE080039.1|EE080039
EST:     GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGCGG                         GTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
genomic: GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGTGGgtaagttttg ... attttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
EST: gi|110701720|gb|EE079612.1|EE079612
EST:     GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGCGG                         GTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
genomic: GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGTGGgtaagttttg ... attttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
EST: gi|37190706|gb|CF610055.1|CF610055
EST:     GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGTGG                         GTACCAAGCCTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC
genomic: GGCCTCAAGAAGCTTGATGAGTACCTCCTGACTAGGAGTTACATCAGTGGgtaagttttg ... attttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaagataatgattaatacatattatgattttgttaaatcattaattttctcagGTACCAAGCTTCAAAGGATGATATCACTGTTCATGCAGCTCTTTCAAAGGCTCCATCATCTGAATACGTGAATGTCTCTAGGTGGTACAACCACATAGAG
                                        cattaat  putative branch site (score: 3)
                                              ttttctc  CT-rich tract
            attaatacatattatg  TA-rich tract