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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagcaaacaaccacatctgaatggattttctaacaatcttaacatttgttcgaatccaacaacaacccatctttgaattctttgtttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT

Basic information

species Vitis vinifera
transcript Vv01s0011g06250.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G09940.1 (Glycine max), 3'ss of exon 2
caagcaaacaaccacatctgaatggattttctaac---aatcttaacatttgttcgaatccaacaacaacccatctttgaattctttgtttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
  |  |    |     ||||  |    |||  |     ||  |  | ||  |  | |||   | || |     |  || | ||| |   || | || || |||||||||||||  || |||||| ||   |||||||||||| | ||||||||||| ||||| |||||||||||||| || ||||||||||||||||||||||
--aaaagttcattgtttctggttttggtttgaagttttaacttacatatccgg-caaatgggataagagtaattaatttatttcatcacttatctgtttgcagATGTCAAATGGTGACATGTTCCAGAATAACCATGATGAAATCGACTTTGAGTTTTTGGGGAACATTAGAGGCAAAGACTGGAGGATTCAGACCAATGTTT

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G01520.1 (Glycine max), 3'ss of exon 2
caagcaaacaaccacatctgaatggattttc-taacaatcttaacatttgttc---gaatccaaca---acaacccatctt--tgaattctttgt-ttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
          |     | ||  | ||||||| |     | |||||   | | |   |||   ||     || |  ||| ||  |  |||| |    || ||    | |||||||||||||  || |||||| ||   |||||||||||  ||||||||||||| ||||| |||||||||||||| || ||||||||||||||||||||||
----------agtttgtttgtctcgattttccttttttttttaactcctttccccagaagataaggggcacgagtcattttaatttattcctaacatttttctgctgcagATGTCAAATGGTGACATGTTCCAGAACAACCATGATGAGATAGACTTTGAGTTTTTGGGGAACATTAGAGGCAAAGACTGGAGGATTCAGACCAATGTTT

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G01520.2 (Glycine max), 3'ss of exon 1
caagcaaacaaccacatctgaatggattttc-taacaatcttaacatttgttc---gaatccaaca---acaacccatctt--tgaattctttgt-ttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
          |     | ||  | ||||||| |     | |||||   | | |   |||   ||     || |  ||| ||  |  |||| |    || ||    | |||||||||||||  || |||||| ||   |||||||||||  ||||||||||||| ||||| |||||||||||||| || ||||||||||||||||||||||
-------gttagtttgtttgtctcgattttccttttttttttaactcctttccccagaagataaggggcacgagtcattttaatttattcctaacatttttctgctgcagATGTCAAATGGTGACATGTTCCAGAACAACCATGATGAGATAGACTTTGAGTTTTTGGGGAACATTAGAGGCAAAGACTGGAGGATTCAGACCAATGTTT

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G26960.1 (Glycine max), 3'ss of exon 2
caagcaaacaaccacatctgaat--ggattttctaacaatcttaacatttgttcgaatccaacaacaacccatctttgaattctttgt-ttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
  |       |     ||||  |  || ||       ||  |  | ||  |  | |||   | || |     |  || | ||| |    || | |  || |||||||||||||  || |||||| ||   |||||||||||| | ||||||||||| ||||| |||||||||||||| || ||||||||||||||||||||||
--aaagggtcattgtttctggttttgggttgaagtctaagttgcatatccgg-caaatgggaaaagagtaattaatttatttcatcacattatctatttgcagATGTCAAATGGTGACATGTTCCAGAATAACCATGATGAAATCGACTTTGAGTTTTTGGGGAACATTAGAGGCAAAGACTGGAGGATTCAGACCAATGTTT

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G27990.1 (Glycine max), 3'ss of exon 2
caagcaaacaaccacatctgaatggattttctaacaatcttaacatttgttcgaatccaacaacaacccatct--ttgaattctttgtttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
 ||  |||   |||  |  |  ||  |    |   | | ||||| | | | |      || |    |     |  || | | ||    || ||    |  ||||||||||||  || |||||| ||   |||||||||||  ||||||||||||| ||||| |||||||||||||| || |||||||||||||| |||||||
-aatgaaaacgcca-gttagtttgtttgcctttttatttttaacttctttccccggaaaatagaggcatgagtaatttattcctcacatttttctgctgtagATGTCAAATGGTGAAATGTTCCAGAACAACCATGATGAGATAGACTTTGAGTTTTTGGGGAACATTAGAGGCAAAGACTGGAGGATTCAGACAAATGTTT

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G14720.1 (Arabidopsis thaliana), 3'ss of exon 2
-caagcaaacaaccacatctgaatggattttctaacaatcttaacatttgtt-----cgaatccaacaacaacccatctttgaattctttgtttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
  ||||||  | |   |      | |||||   |  ||  ||    |||  |      || |  |  ||  ||  |||||  || | |||  |  | |  |  ||| | |||||||  ||  | |  |||   || ||||| ||  | || |||||||| ||||| || ||||||||||  || |||||||||||||||||| | |
gtaagcaacaatctctaatctcttagatttctcatgaaaattgtttttttcttccactgattttagaaagcacaaatcttgaaacttttttatgttct--tctcagTTATCAAATGGGGACTTATATGAGAAGAATCATGACGAGATTGATTTTGAGTTTTTGGGGAATATTAGAGGCAGAGAATGGAGGATTCAGACCAATATAT

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|161721792|gb|FC070495.1|FC070495
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGACGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|161720664|gb|FC069925.1|FC069925
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|161717715|gb|FC065940.1|FC065940
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|161712915|gb|FC062388.1|FC062388
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|71854719|gb|DT003774.1|DT003774
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|110396340|gb|EC962024.1|EC962024
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|30132589|gb|CB917928.1|CB917928
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG
EST: gi|161720549|gb|FC070921.1|FC070921
EST:     CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTAT                         ATGTCAAATGCAGATATGTTCGAGGCAAACCATGACGAACTAGACTTTGAG
genomic: CGATCAAGTTGCCTGCAGATTATACAGCAGGAGTTGTCGTCGCGTTTTATgtgagtaatc ... ttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttcgaatccaacaacaacccatctttgaattctttgtttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT
                                           ctttgat  putative branch site (score: 5)
                                 ttctttgtttcttt  CT-rich tract
                           tttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagcaaacaaccacatctgaatggattttctaacaatcttaacatttgttcgaatccaacaacaacccatctttgaattctttgtttctttgattacagATGTCAAATGCAGATATGTTCGAGGCAAACCATGATGAACTAGACTTTGAGTTCTTGGGTAACATTAGAGGCAAGGATTGGAGGATTCAGACCAATGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
caagcaa
- - - -acaacca
- - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - ctaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaccca