Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttatgaccaactgtatgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA

Basic information

species Vitis vinifera
transcript Vv14s0006g01790.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g32364.1 (Oryza sativa), 3'ss of exon 9
----------------------gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttatgaccaactgtatgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA
                       ||  ||| ||| ||   |||  ||||  ||| | | |   | | | | |||  || |  ||||  ||     ||  |||| || |||   ||||||||||||||||| |||||| |||||||  |||| ||||| || |||||| ||||||| |||||  | ||  |  | || ||||
gtacgccatctgttggttatttctaccgctgatacgaatcata--tatcgattagtacttcagt-tgtgtgcatcgctgaaaaccatttggtc--ttgtagGCGAATTCTGACTGGCTTTACATTGTACCGTGGGGTTTGTACAAAGCTGTCACCTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAA

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os07g46280.1 (Oryza sativa), 3'ss of exon 9
----------------------------------gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttat------gaccaactgtatgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA
                                  ||| |   |  |  |  ||  |  |  ||  |||| | | ||| |||  ||  | | |        |   | || ||     ||||||||||| |  |||||||||||||| |||||||| ||  ||||| |||||||||| || |||||    |||||||||||  | || ||| | || ||||
gtaagtggcagtcaatgtattgtacatttgtacagtagtatgttgaacagttaggaaaagttg--aatttcaagttaaatcatcacacttcaatagttgaattgattgaattcacgcagGCAAACTCCTACTGGCTTTACATTGTGCCATGGGGAATCAACAAGGCTGTGACCTATGTAAAGGAAACATATGGAAACCCTACAATGATCCTTTCTGAAA

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 9
gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttatg-----accaact-----gt---atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA
||||   | |  | |   | |  |||   ||| |   ||  || |  | ||      |||     || || |     ||   || ||| ||||| || |||| ||||||||||| |||||||||||| ||||||||  |  |||  ||| | ||||| |  |||||||||||| || | ||| | || ||||
gtaagtttaaacttagtcacagatattcatta-tatatagatacaagtgcaacaaccatgcattgactaatttgtaagttcaatttttacagGCTAATTCTTATTGGCTTTACAATGTACCATGGGGCATGTACAAATCATTGATGTACATAAAGGAACGTTATGGAAACCCAACTGTTATCTTATCTGAAA

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|349821518|gb|FQ408077.1|FQ408077
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|71867004|gb|DT016059.1|DT016059
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|77585036|gb|DV221603.1|DV221603
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|352777638|gb|FQ466691.1|FQ466691
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|352778016|gb|FQ467069.1|FQ467069
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349833335|gb|FQ416713.1|FQ416713
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349820762|gb|FQ404136.1|FQ404136
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349817382|gb|FQ405386.1|FQ405386
EST:     ATGACCGAGACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|352777869|gb|FQ466922.1|FQ466922
EST:     ATGACGGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349811362|gb|FQ407588.1|FQ407588
EST:     ATGATCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349826361|gb|FQ417858.1|FQ417858
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|351013683|gb|FQ433835.1|FQ433835
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|71867277|gb|DT016332.1|DT016332
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|351028613|gb|FQ446286.1|FQ446286
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|351017081|gb|FQ424508.1|FQ424508
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349807775|gb|FQ402166.1|FQ402166
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349813416|gb|FQ413650.1|FQ413650
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|71866255|gb|DT015310.1|DT015310
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|351029000|gb|FQ435001.1|FQ435001
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|349815167|gb|FQ410390.1|FQ410390
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|351029862|gb|FQ427702.1|FQ427702
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
EST: gi|77578566|gb|DV218076.1|DV218076
EST:     ATGACCGAAACGGGGTGCCAATTGGTCCAAGG                         GCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG
genomic: ATGACCGAAACGGGGTGCCAATTGGTCCAAGGgtaatgctta ... atgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgttaattcctacttatatctacattccttatgaccaactgtatgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA
   tgttaat  putative branch site (score: 3)
                                              tgttttc  putative PPT
             tacttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcttatatgatctataactatctgttaattcctacttatatctacattccttatgaccaactgtatgttttcagGCAAACTCTTTTTGGCTTTACATTGTACCATGGGGTATGTACAAGACTGTGACCTACGTGAAGGAGCAGTATGGAAACCCACCTATAATCATCTCAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG