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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttgtggtccttgtgggagaaaactctcattactcactactcttttatcttctgaaattaaaaggcgaggtggagtataacattttttggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG

Basic information

species Vitis vinifera
transcript Vv11s0016g03530.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g59140.1 (Oryza sativa), 3'ss of exon 2
-------------------tagttgtggtccttgt--gggagaaaactctcattactcactactcttttatcttctgaaat-----taaaaggcgaggtggagtata----acattttttggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG
                    || | | | |  | |   |   || | ||  |||  |   | | |  | | |    | | |     |||| ||| |  ||   |       | ||| | |   |||  |||| || |||||| |  | || ||||| ||||||||||| |||||||| ||||| ||||| | || |||||| |||||||| ||  ||||| |||| ||  
gttagtcctgaacaacaagaagctattgcctctattcagttcaacaatcctattcttttttccccaatgagcactggcatttcacctaaatggctacatgatatgctgcctatattctgtttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC

upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G476009_T01 (Zea mays), 3'ss of exon 2
------------------------tagttgtggtccttgtgggag-aaaactctcattactca--ctactcttttatcttctgaaattaaaaggcgaggtggagtataacattttt--tggct--------ttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG
                         || |      |   |  ||     |    | || ||    |  | |    || | |||   |  || |      ||   | |   |||| |  |  ||          ||||||||| ||  || |  | |||||||| |||||||| ||||||||||||||||||||||| || |  ||||||||||||||  | |||||| |||| ||| 
gtcagttttttgcacaccaagaagaagctactactccaatttgaccggcagcaccgttgcttggtccgcgcgcgcatatgctgttgtgcaatgatctcttgtgttttgttatttctgataactgaagcaatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCT

upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G22320.1 (Arabidopsis thaliana), 3'ss of exon 3
tagttgtggtccttgtgggagaaaactctcattactcactactctt-----ttatcttctgaaattaaaaggcgaggtggagtataacatttt--ttggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG
              ||   | ||| | ||   |  ||   ||||||     | || |    | || | ||  | |  |  |  || |  |  |  | |    | |||||||| ||| || | || ||||| ||||||||||||||||||||||||||||| || || |||| ||| |||||||| ||||| |||||||| || || |
--------------gtaaaacaaatcactttgtg-tcttgactcttgatgatgatgtatccacatcacaatcctac-taaaccatgatttggtggtggatgctgcagGAGGCGGAAATGCTAGTGAACATTAAAGAACATGTTCTTGTTCCTGAGCATCAAGTTCTTACCACTGAAGAGAAGAAAACTTTACTGGAGAGATACACAG

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|351022956|gb|FQ428865.1|FQ428865
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTACTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|352791437|gb|FQ481016.1|FQ481016
EST:     GAACTTGCATTAACGAACTATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|30252036|gb|CB968675.1|CB968675
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTACTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|30329733|gb|CD012995.1|CD012995
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351013267|gb|FQ424972.1|FQ424972
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351013686|gb|FQ433838.1|FQ433838
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|33404617|gb|CF210244.1|CF210244
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTACTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|27585125|gb|CB007820.1|CB007820
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|161713942|gb|FC062890.1|FC062890
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTACTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351014433|gb|FQ437435.1|FQ437435
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTACTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351033523|gb|FQ446989.1|FQ446989
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351041122|gb|FQ444099.1|FQ444099
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|349822801|gb|FQ398188.1|FQ398188
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351022411|gb|FQ445186.1|FQ445186
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGGACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|349818759|gb|FQ409293.1|FQ409293
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|351043644|gb|FQ451575.1|FQ451575
EST:     GAACTTGCATTAACGAACTATCAACAAAATTCCACTTGGAAGTTTTCCAG                         GAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
EST: gi|349820033|gb|FQ404755.1|FQ404755
EST:     GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAG                         AAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT
genomic: GAACTTGCATTAACGAAATATCAACAAAATTCCACTTGGAAGTTTTCCAGgtaaaagttt ... ggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcttctgaaattaaaaggcgaggtggagtataacattttttggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG
                               gtataac  putative branch site (score: 3)
                                       ttttttg  CT-rich tract
                              agtataacatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttgtggtccttgtgggagaaaactctcattactcactactcttttatcttctgaaattaaaaggcgaggtggagtataacattttttggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- -ttgtggt
- - - - - ccttgtg
- - - - - - - - -ggagaaa
- - - - - - - - - - - - actctca
- - - - - - - - - - - - - - - - - ctcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtggag