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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatggctaaatcatactattgcttgtgtcttatataattatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC

Basic information

species Vitis vinifera
transcript Vv14s0108g01230.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 10
-----tatggctaaatcatactattgcttgtgtcttatata-attatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
     |||   |  |   |  ||    |||| | |  |||  ||||| |||| | ||   || | |  |  |   |  |  |   | || ||  | ||     ||||||||||| ||  |||| |||||||||||||| ||| |||||||||||  ||| || ||  |||| ||| ||||  | |||||||  |||||| |  |||
tatagtatcattcgaatgttgtagctgttgtatttggtatgtattatatatatgttgtatatct-ggctgtagaattgctgattccgtttcttttctt-----cagCTTTACAAGACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGACTTCCTTACCAAGC

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g17980.1 (Oryza sativa), 3'ss of exon 10
tatggctaaatcatactattgcttgtgtcttatata-attatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC---------
        |||  |     || |||| | |  |||  ||||| |||| | ||   || | |  |  |   |  |  |   | || ||  | ||     ||||||||||| ||  |||| |||||||||||||| ||| |||||||||||  ||| || ||  |||| ||| ||||  | |||||||  |||||| |  |||         
---attcgaatgttgtagctg-ttgtatttggtatgtattatatatatgttgtatatct-ggctgtagaattgctgattccgtttcttttctt-----cagctttacaagACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGACTTCCTTACCAAGCTGAGGGTTC

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G05700.3 (Glycine max), 3'ss of exon 11
tatggctaa-atcatactattgcttgtgtcttatataattatt--tataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
  |||| ||    || || |||  ||  |  |   |   || |  |||    |  |  |||| | | || | | | | |||    || |  | |     |||||||||||||||||| |||||||| |||||||||||||| || || || ||||||||||| || || ||||||||||| || || ||||||||| | ||||
--tggcaaatgagattctcttgaatgactaattcttgggtagtgctattctttttttttttttacttgagcattctc-aaactcgtgttaatttctttgacagCTTTACAAAACTCGTGAGGAGAAATATCTGCTTGATCTTCAAAGGGTCCAGGGCCCACAGTTTCTTTTCTTGGATCTGTGCGCTGCTTTCCTTTCACAGC

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G49770.2 (Glycine max), 3'ss of exon 10
--tatggctaaatcatactattgcttgtgtcttatataattatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
  || | |  | |    | ||    |   |||| | | ||||||    || |     | ||    ||||  | | |||| ||||  | |  |   | |||||||||||||||| || || || ||||||||||||||||| || || || ||||| ||||| || || ||||||||||| ||||| ||||||||||| ||||
tataagacagattgtctcaataaactaattcttctgttattattgggtagttataattcttttccagaatattctctaattctt-acagtcacatc-aacagCTTTACAAAACCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 10
--------------------------------------------tatggctaaatcatactattgcttgtgtcttatataattatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
                                             | || | |  |     ||    |   |||| | | ||||||    || ||    | ||  |    | |   |   |||  || |    | | | |||||||||||||| | || || || ||||||||||||||||| || || || ||||| ||||| || || ||||||||||| ||||| ||||||||||| ||||
gtaatttacctttagaaccataatgtttataaccaattataagacacggattatcctcttaataaactaattcttctgttattattgggtagttgtaattctttttccagaatattctctaatacttacattcacttc-aacagCTTTACAAAGCCCGGGAAGAAAAGTATCTGCTTGATCTTCAAAGGGTGCAGGGTCCACAGTTTCTTTTCTTGGATCTATGTGCTGCTTTCCTTGCACAGC

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 10
--tatggctaaatcatactattgcttgtgtctt-atataattatttataaggtgctgattt-tgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
  | |  || ||| | |   | |  ||  |||| ||  |  ||  ||| |     |  ||| ||      |   |   |   |  ||| || |  ||  ||||| | || |||||||| || || |||||||| || ||| |||||||||| || || || || ||| | ||||||||||| ||||| ||||| ||||||||||
tttgtaactgaattagaac-tagagtgaatcttcatgaatctaactatcaatcaatattttctgggcttgatgacgtttg--ttattgttgatggtg-aaacagTTGTATAAAACTCGGGACGACAAGTATCTACTGGATTTGCAGAGAGTACAAGGTCCTCAGTTCTTGTTCTTGGATCTGTGTGCTGCTTTTCTTGCTCAGC

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|110375190|gb|EC940152.1|EC940152
EST:     TTGTTGAGAATGATGGTGTTTCCAGGAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAG
genomic: TTGTTGAGAATGATGGTGTTTCCAGGAATGTGGTCAAGTTTGAAGTGCAGgtaatttatc ... ttgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAG
EST: gi|110369736|gb|EC933904.1|EC933904
EST:     TTGTTGAGAATGATGGTGTTTCCAGGAATGTGGTCAAGTTTGAAGTGCAG                         CTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAG
genomic: TTGTTGAGAATGATGGTGTTTCCAGGAATGTGGTCAAGTTTGAAGTGCAGgtaatttatc ... ttgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC
                          ccctaaa  putative branch site (score: 3)
         attttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatggctaaatcatactattgcttgtgtcttatataattatttataaggtgctgattttgattagaacttcccctaaatctttgctgctattgcgaacagCTTTACAAAACTCGAGAGGAGAAGTATCTGCTTGATCTGCAGAGAGTTCAGGGCCCACAATTCCTCTTCTTGGATCTTTGTGCAGCTTTCCTTGCTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
tatggct
- - - -aaatcat
- - - - - - - - - - gcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct