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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgcttaacaagtcattctaaatcttttaacaattttaaggtaccttcaagatgttgaaagtctttagtgtcgtgattttaggtttgtcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC

Basic information

species Vitis vinifera
transcript Vv18s0001g03790.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S427_40V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------gcttgcttaacaagtcattctaaatcttttaacaattttaaggtaccttcaagatgttgaaagtctttagtgtc---gtgattttaggt--ttgtcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC
                                                              ||| |||  | | |||   |  ||        ||||    |       || |||    || |  | ||| ||   ||  || | | |  |  |  || || ||||||||||||| ||||||||||||||| | ||||||||||| |      | || || || |||| |||    || || ||||||||||||||||||||||
gtaagcacctgaaatgttggggcatatatatcgtgggatttcttatggttttaaacagacatttgattagtagg-catcagacttccgcagtttatttccgaggttgagtaaaatg--acaaattgtcagtttccgtgtacttatggatggtctttgttgtgaagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCCGATCAGAAACATTTAGAGAATGGTGAATTTGACGCTGCCAACTCAGAGAAGTTGCGGCTTGAGC

upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------gcttgcttaacaagtcattctaaatcttttaacaattttaaggtaccttcaagatgttga-aagtctttagtgtcgtgattttaggtttg--tcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC
                                                            |||   ||      |  ||     | |  |  || ||   | | |   | ||   || ||  ||||   | |    |  || ||  |||   | |||||| ||||||||||||| ||||||||||||||| | ||||| ||||||||    || || || || ||||||||    || |||||||| ||  |||| ||||| |
gtgagtatctgcaattttcttagacttaaatgcttatactagagatttgacttatatatggctgttttttttctttttttcttttttcctttcagttaataagaaatatgaatcggtagacgagtcaacattcatctacttataaatttaatttattttgtagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTGGAGAATGGTGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC

upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------gctt-gcttaac--aagtcattctaaatcttttaacaattttaaggtaccttcaagatgttgaaagtctttagtgtcgtgattttaggtttgtcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC
                                   |||| |||||||  | | ||   ||||||||||  ||  ||   || | |   |   || |  |  ||||||    | |   |  | |||  |  ||||| ||||||||||||| ||||||||||||||| | ||||| ||||||||    || || || || ||||||||    || |||||||| ||  |||| ||||| |
gtaagtatctgtagtttattcaggcatacactcgagcttcgcttaacttacgccaacgtaaatcttttg-cagcttagtggaaacgatactttggtcga--tctttacccactta--tagatgttgtttgttttgaagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTAGAGAATGGCGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC

upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------------------------gct--tgcttaacaagtcattctaaatcttttaacaattttaa------ggtaccttcaagatgttgaaagtctttag-tgtcgtgattttaggtttgtcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC
                                                                            | |  |  |   ||      |  || || |||   |  |  ||      |||| ||  |     |||  | | ||||| | |           | || || |||||||||| || ||||| || |||||||||||| | ||||||||||| |     || ||  | || |||| |||   ||| |||||||| ||| |||||||||| |
gtaaacatctgaactgtcaagacctgctaatcatctcaaatgttgctgccatttctgaattcttgacagatattccgttgatattcgtcagtctgctgcaattcgtttctgaggtcgaacaaaatggtaactagacaggtttgtcaatgtttagctatttatggagcgtgcttctcgttttgcagGATAAATTGCCACCCACAGATTCAAGGTTGAGACCCGATCAGAAACATCTAGAGCATGGTGAATTTGATGCGGCCAATTCAGAAAAGCTGCGGCTTGAAC

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|161717143|gb|FC068478.1|FC068478
EST:     ACTTAACACGCTTTGCTATCACACTGAATGAGCTCACTCCTGGATTGAAG                         GAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCTGATCAAAGGTGCCTT
genomic: ACTTAACACGCTTTGCTATCACACTGAATGAGCTCACTCCTGGATTGAAGgtgattgtga ... cattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTT
EST: gi|110410950|gb|EC976646.1|EC976646
EST:     ACTTAACACGCTTTGCTATCACACTGAATGAGCTCACTCCTGGATTGAAG                         GAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCTGATCAAAGGTGCCTT
genomic: ACTTAACACGCTTTGCTATCACACTGAATGAGCTCACTCCTGGATTGAAGgtgattgtga ... cattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTT
EST: gi|161719223|gb|FC065737.1|FC065737
EST:     ACTTAACACGCTTTGCTATCACACTGAATGAGCTCACTCCTGGATTGAAG                         GAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCTGATCAAAGGTGCCTT
genomic: ACTTAACACGCTTTGCTATCACACTGAATGAGCTCACTCCTGGATTGAAGgtgattgtga ... cattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcaagatgttgaaagtctttagtgtcgtgattttaggtttgtcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC
                                            tcatttt  CT-rich tract
                              tgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgcttaacaagtcattctaaatcttttaacaattttaaggtaccttcaagatgttgaaagtctttagtgtcgtgattttaggtttgtcattttgcagGAAAAGTTGCCTCCTACAGATTCAAGGCTCAGACCCGATCAAAGGTGCCTTGAAAACGGGGAATATGAAAAGGCAAATTCAGAGAAGTTGCGGCTTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
gcttgct
- - - - - - -gtcattc
- - - - - - - - - - - - - - - aacaatt