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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccaaatatccaaatggtgatgagctattcacaaaacttaaatatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT

Basic information

species Vitis vinifera
transcript Vv07s0130g00270.t01
intron # 10
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 10
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 11
taccaaatatccaaatggtgatgagctattcacaaaacttaaatatgtgcctggtaatccattctgaatcagaacctt-----ggatctttttttggttgaac-------agGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
                 || | |  ||  |  | ||  |||||   |||  |  |   |       || || ||   |     || | | || ||   |  ||       ||||  || |||| ||| | || |||||||||||||||||||| || |||||||||||  | ||||||||||||||| | || || ||||| ||||||||||
-----------------gtaacgtcctgctttctaacattaaaatggtggataattcgcatacagaaaccacaattctcacacggttttcttgttacctcgacgcaacgcagGTGCTGCAGGATAATTTGGAATGGGAGGATGTGCAGTGGTCGCAGACTGGTGTTTGGGTTGCTGGAAAGGAATATCCTCTCGCCCGAGTGCATTTCCTAT

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------taccaaatatccaaatggtgat-gagctattcacaaaacttaaatat---gtgcctggt-aatccattc---tgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
                                                          |     |  || | |  | || |   | || ||  || |||  |      ||| |  | || |  |||   || ||||  |  ||  |   |    | ||||  |||||  ||||||| ||| | |||||||| |||||||| ||||| ||| |||||||||| || ||||||||||||||| | || || || || |||||| | |
gtatttttaaatcacttctcatttattttcaacttgcatgttaaataatgtctcttgaattttctccccgatttattattgcaatgtttactcaaattacgtgcagaatgcatatttaaacttttcaattgtatcaataatttacaatctgcacttgttgtccagGTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAGCTGGTGTTTGGATTGCTGGAAAGGAATATACCCTGGCACGGGTGCATTTCTTGT

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------taccaaatatccaaatggtgatgagctattcacaaaactt---aaatatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
                                                          | |    |     | |  ||    | || ||| |  || |    |||   |   |     | |    || |||| ||  ||  ||  |    | | ||  ||| |  ||||||| ||| | |||||||| |||||||| ||||| ||||| |||||||| || ||||||||||||||| |  | || ||||| |||||| | |
gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataat-ttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 9
taccaaatatccaaatggtgatgagctattcacaaaacttaa-atatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttga-acagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
 |     |  | | ||  || |   ||| | |    ||  ||   |   |  | ||  | ||   ||| | | ||  | | ||  |   ||   |||  |||||  | ||||| || || |||||||| ||||| |||||||| |||||||| ||||| || || |||||||||||| | |||||||| || |||||| | |
-aatttgtggctatatattgttattctaattaatttacagaatgcaaacgtattgtgtttcaacttga-ttataaattcgaattctgcattttctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 10
taccaaatatccaaatggtgatgagctattc-acaaaacttaaatatgtgcctg-gtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
  |  ||| |       ||       ||||| |   || |  |  |||    ||  |  | ||   ||| | | ||       |||   |||  |    |||||  | ||||| || || |||||||| ||||| |||||||| |||||||| || || || || |||||||||||| | |||||||| || |||||| | |
-tctcaat-ttggtgctgtataattttattctaatgaattccagaatgcaaatgtatgtttcaacttgattaaaaattccaattctgcattttctaatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCACAAACTGGCGTCTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT

upper sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
taccaaatatccaaatggtgatgagctattcacaaaacttaaatatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
     || ||     |     |   || |||       || || ||         ||   || ||||    |     |||||   |||    | ||  |||| |||||||||||||| || ||||| ||||| |||||||| |||||||||||||| || |||||||| || ||  | |||||||| |||||||| || |
--gttaacatttttctccaatttgactcttcttgt--tttgaaaattctttataaaacaaatgctgatgatgtgttgtggat---tttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT

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:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|110420000|gb|EC986260.1|EC986260
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|110717059|gb|EE092582.1|EE092582
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAAAATCTCGACTGGGAAGATGTGCAGTGGTCCCCAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|30304050|gb|CB980844.1|CB980844
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|110422711|gb|EC989039.1|EC989039
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|30133283|gb|CB918622.1|CB918622
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|30304255|gb|CB981049.1|CB981049
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|51050997|gb|CO818834.1|CO818834
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
EST: gi|110406983|gb|EC972573.1|EC972573
EST:     AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAG                         GTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT
genomic: AAAAAGTCATGCGTTCACTGGGAATCCCACTGCCCCTCGAACATTTAGAGgtacttcgtc ... ggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT
                                    tctttttttg  CT-rich tract
                                   atcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccaaatatccaaatggtgatgagctattcacaaaacttaaatatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
taccaaa
- - - - atccaaa
- - - - - - - - ggtgatg
- - - - - - - - - - - - - - - -acaaaac
- - - - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaacc