Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaattttgtggttcaaaatgaagctatatagtattagatttactctaaattatttagttttattcacagtttttccttctgcctttctgggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGAT

Basic information

species Vitis vinifera
transcript Vv17s0000g06190.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G10820.1 (Glycine max), 3'ss of exon 1
----------------------------------------ttaattttgtggttcaaaatgaagctatata---gtattagatttactctaaat-tatt----tagttttattcacagtttttccttctgcctttctgggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGAT
                                        | | || |||| ||  | ||     || | |    | || | |||  |   ||  |||     || ||   |||  |   | |   |   | ||  |   ||||  |||| || | |||||||| ||||| |||||||||||||||||||| ||||| || || ||||||||||| ||||| || || || || || ||||||| |||
gtagtttttattttcaactcttctctttttcattcagttttcatttctgtgtttatatatagctttacacacacatttttgcttttttgggaaggtataggagtaattgatttcgtacactatatattaactttcattttttttcaagGTTTGATGAGATGCAGCAAGAGCTGCAGGCTTAGATGGACTAACTATCTTCGACCTGGTATCAAACGAGGTAATTTCACGGAACATGAAGAGAAGATGAT

upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G01080.1 (Glycine max), 3'ss of exon 1
-----------------------------------ttaattttgtggttcaaaatgaagctatata---gtattagatttactctaaattatttagttttattcacagtttttccttctgcctttctgggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGAT
                                   ||  |||  |   |     |  |||| || |    |||| | ||      ||  ||| || ||   |||  |   | |   | |  |||||    ||||| |||| || | |||||||| ||||| |||||||||||||||||||| ||||| || || ||||||||||| ||||| || || || || || ||||||| |||
gtatagttttcaggttcaattgttatctatttattttcttttcatttctgtgcttatagctttacacacatatttgtttcttgggaaggtatataattgatttcgtacactatatat-taactttcactttttttaagGTTTGATGAGATGCAGCAAGAGCTGCAGGCTTAGATGGACTAACTATCTTCGACCAGGTATCAAACGAGGTAATTTCACGGAACATGAAGAGAAGATGAT

upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G20800.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------ttaattttgtg--gttcaaaatga------agctatatagta------ttagatttactctaaat-tatttagttttattcacagtttttccttctgcctttctgggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGAT
                                                                         ||||||||||  | |    |         |  | | || ||      | ||    | |  |  | | | |  | |  |  |   ||        |   ||| | |||||||||||| || | |||||||| || || ||||| || |||||||| || |||||||| || ||||||||||| || || || || ||||| || ||||| | |||
gtaataaaaattcaaccttaaatttaacatatggttttgatttaatttcttcatttatttgttgggtttttcataattttgtgcagctgggcaccgtttattaattgtttaataaatcggtgagggacagtacatgtatgtatgatgtagtatatgattccattaattttgttttttggtttttcagGTTTGATGAGATGCAGCAAAAGCTGCAGACTCAGATGGACCAACTATCTCCGACCTGGTATCAAACGAGGCAATTTCACCGATCATGAAGAGAAAATGAT

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|71859434|gb|DT008489.1|DT008489
EST:     CATTCAAGATCATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAG                         GTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
genomic: CATTCAAGAACATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAGgtttaatatt ... ggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
EST: gi|110686690|gb|EE064618.1|EE064618
EST:     CATTCAAGATCATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAG                         GTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
genomic: CATTCAAGAACATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAGgtttaatatt ... ggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
EST: gi|294965744|gb|GW839199.1|GW839199
EST:     CATTCAAGAACATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAG                         GTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
genomic: CATTCAAGAACATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAGgtttaatatt ... ggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
EST: gi|33408386|gb|CF214013.1|CF214013
EST:     CATTCAAGAACATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAG                         GTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC
genomic: CATTCAAGAACATGGTCCAGGGAATTGGAGAGCAGTTCCTACTAGCACAGgtttaatatt ... ggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaattatttagttttattcacagtttttccttctgcctttctgggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGAT
 ctctaaa  putative branch site (score: 3)
                         tttttccttctgcctt  putative PPT
     ttatttagttttattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaattttgtggttcaaaatgaagctatatagtattagatttactctaaattatttagttttattcacagtttttccttctgcctttctgggtttttcagGTCTGCTTAGATGCAGTAAGAGTTGCAGGCTTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - ttgtggt
- - - - - - - - aaatgaa