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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaattcactttttcttttatttcttatttggatggaatatgtagctcatctgataaaatcatgaggtggaatgtttaacaaaatttattgtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC

Basic information

species Vitis vinifera
transcript Vv11s0016g04250.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 4
gcaattcactttttcttttattt-cttatttggatggaatatgtagctcatctgataaaatcatgaggtggaatgtt-taacaaaatttattgt-ctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC
   |||   || | ||  ||| |  || |    |||   |      ||    ||  ||||  ||  |  | ||  ||  |  || | || || | ||    |||||||  |||| ||||||||||| || |||   ||||||||||| || || |||||||| |||||||| || ||||||||| | || |  |  |||||| 
---attggtttatactcctatctgtttgtaaaaatgctgtcctatcctgggttggaaaaacaatttgcggcaaaattgcatgaagacttgttttgctttgtagTTTGAAGAGAAGGCAAATGAGGTTGTTGCAGCACTTCCTTGGGTCAAGAAGGTCAATGTTACAATGTCTGCGCAACCTGCACGACCAGCATACGCAGGGG

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 4
gcaattcactttttcttttatttcttatttggatggaatatgtagctcatctgataaaatcatgaggtggaatgtttaacaa--aatttattgtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC
  |  |  | || |     |     | ||| | |     || |  | ||||    |   | |||   ||   ||  ||  ||  ||| |||   |   ||||||||||||||| |||||||| |||||||||||||| |||||||| || ||||| || || |||||||| |||||||| ||||| ||  | | ||| | ||
-tatcttccattatagagaaagaaatgtttcg-tacttgattttccccatccctaattctaatgtattgatttgactatgaatgaatatatatgcatgacagTTTGAGCAGAAGGCAAATGAAGTGGTGGCAATGCTCCCTTGGGTCAAGAATGTAAAAGTTACAATGTCTGCACAACCAGCAAGACCCATATATGCTGAGC

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 4
gcaattcactttttcttttatttcttatttggatggaatatgtagctcatctgataaaatcatgagg-tggaatgtttaacaaaatttattgtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC
  | |||| | | ||||  |||    |    ||     |  |||  | || |     |    | |   |    |||| |  | | | |||   |   ||||||||||||||| |||||||| |||||||||||||| |||||||| || ||||| || || |||||||| |||||||| || || ||  | | ||| | ||
atatttca-tctatcttccattatagagaaagaaatgtttcgtacttgattttccccatctttaaatctaatgtgttgattagactatatatgcatgacagTTTGAGCAGAAGGCAAATGAAGTGGTGGCAATGCTCCCTTGGGTCAAGAATGTAAAAGTTACAATGTCTGCACAACCAGCTAGACCCATATATGCCGAGC

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------gcaattcactttttcttttatttcttat--ttggatggaatatgtagct----catctgata---aaatcatgaggtggaatgtttaacaaaattt----------attgt-----ctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC
                                ||  | |||  |  |   | ||| |    || |  ||| | || ||||    |||  | ||   ||   ||||    |    ||||    |  ||          |||        |    |||||||| | || ||||||||||| || |||   ||||| ||||| || || || ||||| ||||||||||||||||| || | |||  ||||||||||||
gtaaatgacattaccattcactattcttttatcatattactactgatagaacttcatcccattaggaggattttggagctatatcattggttatataagcaatgaatcagttcttttagtgtatctttgatggatggattacgactcttttgtagTTTGAGAACAAGGCAAATGAGGTAGTTGCAGCCCTTCCATGGGTGAAGAAGGTAAATGTGACAATGTCAGCACAACCAGCCAAGCCCATTTTTGCAGGGC

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|352777419|gb|FQ474053.1|FQ474053
EST:     TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATG                         TTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT
genomic: TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATGgtaaataaaa ... gtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT
EST: gi|352773640|gb|FQ472422.1|FQ472422
EST:     TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATG                         TTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT
genomic: TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATGgtaaataaaa ... gtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT
EST: gi|352764180|gb|FQ471160.1|FQ471160
EST:     TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATG                         TTTGAGCAGAAAGCAAATGAGGTGGAGGCAATGCTTCCTTGGGTAAAAAAT
genomic: TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATGgtaaataaaa ... gtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT
EST: gi|352776504|gb|FQ474806.1|FQ474806
EST:     TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATG                         TTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT
genomic: TTTCATTTCGGTTAGAGCTCACTACACCAGCATGTCCAATCAAGGACATGgtaaataaaa ... gtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatctgataaaatcatgaggtggaatgtttaacaaaatttattgtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC
                            gtttaac  putative branch site (score: 3)
                                           ttgtctc  putative PPT
                         aatgtttaacaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaattcactttttcttttatttcttatttggatggaatatgtagctcatctgataaaatcatgaggtggaatgtttaacaaaatttattgtctcaacagTTTGAGCAGAAAGCAAATGAGGTGGTGGCAATGCTTCCTTGGGTAAAAAATGTCAATGTAACAATGTCAGCACAACCTGCAAGGCCTGTTTTTGCAGGGC

-caattca
- - - - - - - - - - - - - - -tggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa