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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacatttggctgtccacatgtgattttacattcctttgttgcttattttctttgttatcatctcaagatgcccaatcattgatttatgcttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC

Basic information

species Vitis vinifera
transcript Vv01s0010g03700.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G00920.2 (Glycine max), 3'ss of exon 2
tgacatttggctgtccacatgtgattttacattcctttgttgcttattttctttgttatcatctcaagatgcccaatcattgatttatgcttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC----------------
                                                              || ||| |         || |||  |  || || ||||||||  | || |||||||||||||| || || |||||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| || ||||| || ||                
-------------------------------------------------------------cctaaagttagatgcattttaattggtttttgtctgtaggtagtcgtagggaagatgattggacatgccccagctgtggtaatgttaatttctctttcagGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCCGGCTGATCATAATTCT

upper sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G00920.1 (Glycine max), 3'ss of exon 2
tgacatttggctgtccacatgtgattttacattcct--ttgttgctt----attttctttgttatcatctcaagatgcccaatcattgatttatgcttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC
     ||  |||    |  ||| |||  | |||| |  ||| || ||    ||  |||    |   | || ||| |         || |||  |  || || ||||||||  | || |||||||||||||| || || |||||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| || ||||| || ||
-----ttatgctactaatttgtaattcaa-attcttacttggtgtttgtggatgatctggagttgaacctaaagttagatgcattttaattggtttttgtctgtagGTAGTCGTAGGGAAGATGATTGGACATGCCCCAGCTGTGGTAATGTTAATTTCTCTTTCAGGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCC

upper sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G36990.3 (Glycine max), 3'ss of exon 2
tgacatttggctgtccacatgtgattttacattcctttgttgcttattttctttgttatcatctcaagatgcccaatcattgatttatgcttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC
  ||| |   |          |  ||||  | | |  |||||   ||  | |    |   | || ||            ||  ||  |  || |  ||||||||  | || |||||||||||||| || || |||||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||| || ||||| || ||
ccacactcaccatcgtgttactttttttgtaattcaatgttgtggatgatgtggtgttgaacctaaactcaggtgcattttatttggtttttgtttgtagGTAGTCGTAGGGAAGATGATTGGACATGCCCCAGCTGTGGCAATGTCAATTTCTCTTTCAGGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCC

upper sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G67325.2 (Arabidopsis thaliana), 3'ss of exon 3
tgacatttggctgtccacatgtgattttacattcctttgttgcttattttctttgttatcatctcaagatgcccaatcatt-gatttatgcttat--ccgtagGTAGCAGG----AGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC
            |||    | |        ||   ||| |      ||||   | |||   |  ||| |||   | |  || | ||||| ||| |   ||| | |||  ||    |||||||||||||||| ||| || || ||||||||||| || ||||| || ||||| |||||||||||||| ||||| || || || |||||
-------ctatagtcagtttctttcagcgtatatgtttataaagggtttttgattttagactaccaatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC

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|34415810|gb|CF414564.1|CF414564
EST:     GTAGATACCAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAGGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|349808005|gb|FQ402396.1|FQ402396
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|349807671|gb|FQ402062.1|FQ402062
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|71858373|gb|DT007428.1|DT007428
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|349814507|gb|FQ399147.1|FQ399147
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|349815268|gb|FQ400423.1|FQ400423
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|110381005|gb|EC946312.1|EC946312
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
EST: gi|352777438|gb|FQ474072.1|FQ474072
EST:     GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATG                         GTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT
genomic: GTAGATAACAGGAATTCTTCAGCTGCCAAGCGAGCACGAACTGATGgtatgatagt ... ttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctttgttatcatctcaagatgcccaatcattgatttatgcttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC
                                cattgat  putative branch site (score: 4)
                                            cttatcc  putative PPT
                             aatcattgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacatttggctgtccacatgtgattttacattcctttgttgcttattttctttgttatcatctcaagatgcccaatcattgatttatgcttatccgtagGTAGCAGGAGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC

- - - - - ctgtcca
- - - - - - - - -catgtga
- - - - - - - - - - - - - - acattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaatca