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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctaatctgcaaagttataatacttatgttattgttgtcattgttataaggttcttggtcacataatctgattctaaatttcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT

Basic information

species Vitis vinifera
transcript Vv03s0017g00540.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G32980.1 (Glycine max), 3'ss of exon 2
tttctaatctgcaaagttataatacttatgttattgttgtc-attg---ttataaggttcttggtcacataatctgattctaaatttcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
         |    |||||||    ||   || | | ||   | ||   | |||| || | |  || ||    ||    |   |||||   ||     || ||| |  |||||||||||| ||||||||| ||||||||||||||
-------gttaattagttatagccattgaattgtagatgctgactgaactaataatgtccgttttctcacttccttgaacctgatttcatgcattgctttacagGTTCTGGAGTATTGGGTTGGCAGGGGTATGCTGCAGATTTT

upper sequence: Vv03s0017g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G30080.1 (Glycine max), 3'ss of exon 2
--tttctaatct-gcaaagttataa-tacttatgttattgt---tgtcattgttataaggttcttgg----tcacataatctgattctaaatt-tcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
  ||||   | | ||  | |||| | | | |  |||  |     |     | || |||   || ||     || |||  || | |   | ||  | ||        || ||| | |||||||||||||||| |||||| ||||||||||| ||
gttttccgttttcgcttacttattactgcctccgttcctaaacataaggctcttttaacactcgtgctgtttcgcatgctccgttatgatataattgaatggtcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT

upper sequence: Vv03s0017g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G07230.1 (Glycine max), 3'ss of exon 2
-tttctaatctgcaaagttat-aatacttatgttattgttgtcattgttataaggttcttggtcacataatctgattctaaatttcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
 || |   |  ||  |||| | || ||| | ||   ||||     || | |    |   | || || |||  ||| |     || |        | | |||| | |||||||||||||||| |||||| ||||||||||| ||
gttccgttttcgcttagttgttaacactcacgt-gctgtttcgcgtgctctgttatgacttgtgacctaaattgaat----gttcc--------tttagcagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT

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|161706214|gb|FC054972.1|FC054972
EST:     GCTGAGACGGAGTGGGGATTCATCATGAAG-TCTGGAAG                         ATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
genomic: GCTGAGACGGAGTGGGGATTCATCATGAAGTTCTGGAAGgtttgtttct ... catgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
EST: gi|71863897|gb|DT012952.1|DT012952
EST:     TTGTGGTTGTTGCTGAGACGGAGTGGGGATTCATCATGAAGTTCTGGAAG                         ATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
genomic: TTGTGGTTGTTGCTGAGACGGAGTGGGGATTCATCATGAAGTTCTGGAAGgtttgtttct ... catgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataaggttcttggtcacataatctgattctaaatttcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
                            ttctaaa  putative branch site (score: 2)
                           attctaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctaatctgcaaagttataatacttatgttattgttgtcattgttataaggttcttggtcacataatctgattctaaatttcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - ctgcaaa
- - - - - - - - - - - - - - - - - tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc