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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcattggttttgcgatttttctttatgggttttgattttagatccatgattcgtgggaatgaattgatttttggtgcaaattggttgaatttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAGTAGCAGCGCTGCATAAATACAAGTACAGTGGAGTGGATCACTCGTATGT

Basic information

species Vitis vinifera
transcript Vv01s0010g00950.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 1
-tttcattggttttgcgatttttctttatgggttttgattttagatccatgattcgtgggaatgaattgatttttggtgcaaattggttgaatttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAGTAGCAGCGCTGCATAAATACAAGTACAGTGGAGTGGATCACTCGTATGT------------
   | |  |  | ||  |  |    | | |     || ||| |  ||  ||     |  ||||  |  ||| | | ||     ||| ||   ||  | |||| |            || ||  || |||| | ||||||||| | ||||| |||||||| || ||||  ||||| |||||||||||||||||||| ||| |            
gcattagggaatatgaaaagtgctctcaagatccatgctttaatgtcattgtgggattagaattgag-gatatcttgtttttgttgttttgtttgaatcagTGT------------GATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTCATAGGTACAAATACAGTGGAGTGGATCACTCTTATCTTGCCAAATACGT
















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|351028084|gb|FQ425985.1|FQ425985
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|351043445|gb|FQ444045.1|FQ444045
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|37184688|gb|CF604042.1|CF604042
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|349829684|gb|FQ421202.1|FQ421202
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|349824351|gb|FQ417738.1|FQ417738
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|110708043|gb|EE085132.1|EE085132
EST:     CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|110694296|gb|EE071276.1|EE071276
EST:     CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAA                         TTTCCGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|351040557|gb|FQ434690.1|FQ434690
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|351014955|gb|FQ444244.1|FQ444244
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|351029069|gb|FQ435269.1|FQ435269
EST:     CCGGACACAGAAAAACTTCACCTTTGATC-AACCTGTGCAATCCAAGAAA                         TTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CCGGACACAGAAAAACTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
EST: gi|110687900|gb|EE065836.1|EE065836
EST:     CTTCACCTTTGATCTAACCTGTGCAATCCAAGAAA                         TTTCCGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG
genomic: CTTCACCTTTGATCTAACCTGTGCAATCCAAGAAAgtaaagttct ... atttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgattcgtgggaatgaattgatttttggtgcaaattggttgaatttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAGTAGCAGCGCTGCATAAATACAAGTACAGTGGAGTGGATCACTCGTATGT
                  aattgat  putative branch site (score: 4)
              aatgaattgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcattggttttgcgatttttctttatgggttttgattttagatccatgattcgtgggaatgaattgatttttggtgcaaattggttgaatttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAGTAGCAGCGCTGCATAAATACAAGTACAGTGGAGTGGATCACTCGTATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - ttatggg
- - - - - - - - - - - - - - - - - - - - - - -ccatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttga