Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctttggccaaacttgaagttgcattttgtcctatacatgtgcaattgatgccttgacattgcagatcttcactactgagacactgagttattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATAGGGAACTCTGTTGGGAGTCTTGCTTGTGTCATTGCTGCCTCAG

Basic information

species Vitis vinifera
transcript Vv18s0089g01420.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g01420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G35660.1 (Glycine max), 3'ss of exon 2
gtatatctttggccaaacttgaagttgcattttgtcctatacatgtgcaattgatgccttgacattgcagatcttca----ctactgagacactgagttattct---acagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATAGGGAACTCTGTTGGGAGTCTTGCTTGTGTCATTGCTGCCTCAG
|||| | |||    |   || || | |   |     ||  |  | |    |   ||  |  |  || |||   | ||    | |||   || | |  ||   |    |||||| || |||||||||||| ||||| ||||||  || |||||||| || ||||| ||||||||||| || |||||||||||||||||||||||||
gtatttatttattgaggttttaattggagataaactctccagcttttttgtgtgtgtgtgaaatttccagcattacaaactcaacttgtacccggtattcaccgtaaacagTTGATCTTGGATTTCTTGAATGAAGTTGTTCAGAAGCCAACTGTACTAATAGGAAACTCTGTTGGAAGCCTTGCTTGTGTCATTGCTGCCTCAG

upper sequence: Vv18s0089g01420.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G38520.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatatctttggccaaacttgaagttgcattttgtcctatacatgtgcaattgatgccttgacattgcagatcttcactactgagacactgagttattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATAGGGAACTCTGTTGGGAGTCTTGCTTGTGTCATTGCTGCCTCAG
         |   ||| |||  |  | |  | || | | |   |||    || | |   ||   | |      ||   |  |||     |   || |  |  |||| ||| |  | |||||||| ||| | ||||  ||||| ||| |  |||| || ||||||||||| || |||||||||||||| ||||||||||
--------gtaaacaatctttgaaatac--tctggcatgtttttgt-tgtttaaagaagtgttttggtttggtttggtt--tgatttgatttattttggtgtagTTGATACTCAACTTCTTGGAGGAAGTGGTTCAGAAACCGACTATTTTGATTGGAAACTCTGTTGGAAGCCTTGCTTGTGTCATCGCTGCCTCAG
















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|110376208|gb|EC941257.1|EC941257
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|110708386|gb|EE085867.1|EE085867
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|351012301|gb|FQ429986.1|FQ429986
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|26264357|gb|CA815420.1|CA815420
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|77584623|gb|DV221395.1|DV221395
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|110711535|gb|EE088128.1|EE088128
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATTTTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|110712201|gb|EE089554.1|EE089554
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATTTTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|352790430|gb|FQ478070.1|FQ478070
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|352798352|gb|FQ480377.1|FQ480377
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|351038339|gb|FQ461031.1|FQ461031
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
EST: gi|351048153|gb|FQ442123.1|FQ442123
EST:     CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAG                         TTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA
genomic: CATCTGATAAGCCATCAGGCTTTGCATATACAATGGAAATATGGGCTCAGgtatatcttt ... tattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatgccttgacattgcagatcttcactactgagacactgagttattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATAGGGAACTCTGTTGGGAGTCTTGCTTGTGTCATTGCTGCCTCAG
       ccttgac  putative branch site (score: 4)
                                            ttattct  putative PPT
                                            ttattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctttggccaaacttgaagttgcattttgtcctatacatgtgcaattgatgccttgacattgcagatcttcactactgagacactgagttattctacagTTAATATTGGATTTCTTGGATGAAATTGTTCGTAAACCAACTGTGCTGATAGGGAACTCTGTTGGGAGTCTTGCTTGTGTCATTGCTGCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC