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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT

Basic information

species Vitis vinifera
transcript Vv09s0002g00340.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
                    ||||| || | ||| || ||    ||  |||||    |   |   |  |  |  |||  ||  |  | |  ||||||    |||| |||||||| |||||||| ||||||||||| ||||||||| | ||||| ||  | |||   ||  | || ||||| |||||  | || || ||||| ||
------------------gtaaatttat-ataaccagctactttat--ctgccttttggccaagtaact--ggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G05130.1 (Glycine max), 3'ss of exon 11
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgct-ggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
||| |||| |   |  |    |||| || | ||||||| ||   |  |||   |    ||| |  | |    ||| |   |  |||  | |||  | | | ||||| ||  | ||||||||||| ||| |||||||||| |||||||| |||||||||   || || ||| ||||||| ||||| |||||||||||||| || ||
gtaagttggtaccagaatt--aattaattataacaagagagacta-gacttttatgctaatttataatccatattgatggaagatgcctttttctttgtcctcagGCTATCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGTTTTCTGCAGAAGTGAGGGAACAAATATATAAAGTGGCATCTGTCAACCT

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G01630.2 (Glycine max), 3'ss of exon 9
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgct-ggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
||| |||| |   | ||   || |   | | ||||||| ||   | |  |    |   | || ||| |    ||| |   |  |||||| | |  | | | ||||| ||| | ||||||||||| ||| |||||||||| |||||||| |||||||||   || || ||| ||||||| ||||| |||||||||||||| || ||
gtaagttggtacaa-caattaattaattaataacaagagagactagacttttatgctaattaatga-tccatattgatggaagatgtgtttctctttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGTTTTCTGCAGAAGTGAGGGAACAAATATATAAAGTGGCATCTGTCAACCT

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
     |||||   |  |  |||||   | |       || |  |||      ||     ||    |  | |     || | | ||   |  || ||| |   |||||||||||| |||||||| |||||||| |||||||||||||| ||||| ||     |||||||  | || |||||||||||| |||| |||||||||||
---gtttgatacaa--aaacaaatctcttagtc---aattgataattctgatcattgcgatgggaaactagtcagaaaactgaattcattatttctgac---agGGTACTATGGAGAGTGTGGGAAAAGAGGTGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAGCAGATATACAAAATGGCTTCTGTGAATCT

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
                 |  |||  || |||       |    |||   || ||    || | || | ||   |||  |    || |   | || ||     ||| || ||||| || ||||||||||||||||||||||||||||| ||||| ||     |||||||  | ||||||||||||||| |||| |||||||||||
-----------------gtaaaa--gaacaacttttactgtccaatgcttgtcatctaaaaaatggggtt---tttgtttttaatattcttctgttgat---agGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT

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|110416246|gb|EC982214.1|EC982214
EST:     GTATGGCGAGGAAGATATCTCTGTAGTATCATTTCAGTCAGTCTCTAAAG                         GGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGT
genomic: GTATGGCGAGGAAGATATCTCTGTAGTGTCATTTCAGTCAGTCTCTAAAGgtatgttgat ... ctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGT
EST: gi|110723347|gb|EE100553.1|EE100553
EST:     GTATGGCGAGGAAGATATCTCTGTAGTATCATTTCAGTCAGTCTCTAAAG                         GGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGT
genomic: GTATGGCGAGGAAGATATCTCTGTAGTGTCATTTCAGTCAGTCTCTAAAGgtatgttgat ... ctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
                       atttaat  putative branch site (score: 4)
                                       tctttgct  putative PPT
      aagaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT