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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatttatcaaatcattttttcccttaaccgtgttctaaatgttctattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG

Basic information

species Vitis vinifera
transcript Vv01s0010g01180.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA0042S00440.1 (Glycine max), 3'ss of exon 3
---------ggatttatcaaatcattttttcccttaaccgtgttctaaatgttctattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG
           ||   |    ||  | | |||  |||   | ||  |||| || |  ||   |      ||     |  | ||| || ||| | |||      |||||||||||  |||| ||||| ||| ||||| |||| |||||||||||||| || ||| | |||||| |||| || |||
gctccttgcaaatagttaccgtctatctatcctctaatactatttcaaatttttttctcccgt------aattggcattgctctcaaagttgtctttggt---ctgcagTGTGGGCTAGGGGATGCTTTCAGGTGCAGTACCTGCCCTTACAAGGGACTGCCTGCCTTCAAATTGGGCGAGAAG

upper sequence: Vv01s0010g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G17560.1 (Glycine max), 3'ss of exon 6
----------ggatttatcaaatcattttttcccttaaccgtgttctaaatgttctattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG
          | ||   |    ||  | | |||  |||   | ||  |||| || | | |          ||     |  | ||| || ||| | |||      |||||||||||  |||| ||||| ||| ||||| |||| |||||||||||||| || ||| | |||||| |||| || |||
tgctccttgcgaatagttaccgtctatctatcctctaatactatttcaaattttttctcccgt-------aattggcattgctctcaaagttgtctttggt---ctgcagTGTGGGCTAGGGGATGCTTTCAGGTGCAGTACCTGCCCTTACAAGGGACTGCCTGCTTTCAAATTGGGCGAGAAG

upper sequence: Vv01s0010g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G10960.1 (Glycine max), 3'ss of exon 6
--------ggatttatcaaatcattttttcccttaaccgtgttctaaatgttctattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG
           | ||| |  ||| | | |||  |||   | ||  | || || |        |||     |   |     ||| || ||| | |||      |||||||||||  |||| ||||| ||| ||||| |||| |||||||||||||| || ||| | |||||| |||| || |||
aatagttaccctctattatgtcaatctatcctctaatactatttcagatttttttcctcccataattggcattga-----tctcaaagttgtctttggt---ctgcagTGTGGGCTAGGGGATGCTTTCAGGTGCAGTACCTGCCCTTACAAGGGACTGCCTGCCTTCAAATTGGGCGAGAAG

upper sequence: Vv01s0010g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G18400.3 (Arabidopsis thaliana), 3'ss of exon 7
--ggatttatcaaatcattttttcccttaaccgtgttctaaatgttctattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG
      || |  |  ||| | || |    |   ||   |  || ||   ||| |      || |   ||||  |  ||||   ||  ||          ||||||||  | || ||||||||||| |||||||||||||||||||||||||| || || |||||| | || || |||
gtaagcttctttacccatctctttctc--agtatgcattggatttttggttccac-----aagactgaaaatttcttaaacaattcttt----------cagTGTGGGCTCGGTGATGCCTTCCGCTGCGGTACATGCCCTTACAAGGGTCTGCCACCCTTCAAATTAGGCGAGAAG

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|352786781|gb|FQ481156.1|FQ481156
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
EST: gi|351017704|gb|FQ436057.1|FQ436057
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTATAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
EST: gi|110383767|gb|EC948165.1|EC948165
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGAACATGCCCTTACAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
EST: gi|349813601|gb|FQ413835.1|FQ413835
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
EST: gi|349811637|gb|FQ409634.1|FQ409634
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
EST: gi|32459622|gb|CD800796.1|CD800796
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGACAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
EST: gi|110385198|gb|EC949701.1|EC949701
EST:     TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGT                         TGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT
genomic: TAGGTCTGACTATGGATCAATTGAACAATCCTCAGTCAGCATGTGGAAGTgtatgtccga ... catcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG
                          ttctaaa  putative branch site (score: 2)
     taattaaaaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatttatcaaatcattttttcccttaaccgtgttctaaatgttctattctaattaaaaaaaaaaaaaaagttctaaatgttttattttacatcctgcagTGTGGATTAGGAGATGCCTTCCGGTGCGGTACATGCCCTTACAAGGGTCTTCCTCCATTCAAACTGGGGGATAAG

- - - - -aaatcat
- - - - - - - - - - -cccttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa