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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtgtaatcactgcaagttcatgctaatgatattattgaagtttgatgaacctctatgtaatgtctttttgctttctaatctttgggattgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATTGCATGGACATGAAACAGAGACAGAGAAATCTCAGACTCATAGCTTGCAT

Basic information

species Vitis vinifera
transcript Vv07s0130g00270.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 10
atggtgtaatcactgcaagttcatgctaat----gatattattgaagtttg--atgaacctctatgtaatgtctttttgctttctaatctttgggattgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATTGCATGGACATGAAACAGAGACAGAGAAATCTCAGACTCATAGCTTGCAT
 |||| |  ||  || |  ||| ||  | |    ||| || |||||||||   |  ||| ||    |  |||  ||||  |  | | |     |  || | || || |||||||| ||||||| |||||||||||||||||| | |||| |||||   ||    |||||  | |  ||||| || ||||| | |||   |   |||
ttggtctgttccatg-atcttcttgaaagtctgagatcttgttgaagtttagaagaaacttcctactgctgttcttttaataacaagt-----gatttctgtgtagATATGAACTTTGTTTTACTGGAGAGAAGATGGTCAAGGTTACACCAGCAACCCAGTTGCATGACCCTGTCACAGAAAAGTCTCAAAATCACCACCCACAT
















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|30303985|gb|CB980779.1|CB980779
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|37186804|gb|CF606157.1|CF606157
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|110420000|gb|EC986260.1|EC986260
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|110717059|gb|EE092582.1|EE092582
EST:     GCACGCTTGAAGAAAGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|30304050|gb|CB980844.1|CB980844
EST:     GCACGCTTGAAGAAGGGAGAAGTNTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|110422711|gb|EC989039.1|EC989039
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|30133283|gb|CB918622.1|CB918622
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|30304255|gb|CB981049.1|CB981049
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|51050997|gb|CO818834.1|CO818834
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
EST: gi|110406983|gb|EC972573.1|EC972573
EST:     GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAG                         GTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT
genomic: GCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACACATTCCCGCAGgtattcactt ... ttgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgaacctctatgtaatgtctttttgctttctaatctttgggattgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATTGCATGGACATGAAACAGAGACAGAGAAATCTCAGACTCATAGCTTGCAT
                              ttctaat  putative branch site (score: 2)
           tatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtgtaatcactgcaagttcatgctaatgatattattgaagtttgatgaacctctatgtaatgtctttttgctttctaatctttgggattgtctgaagGTATGAACTGTGTTTTATTGGAGAGAAGATGGTCAAAGCTACAACAGCATTGCATGGACATGAAACAGAGACAGAGAAATCTCAGACTCATAGCTTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
-tggtgta
- - - - - cactgca
- - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctctatg