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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 19
cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgat-ttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
    || | | |   ||| |   |   |  | |||    |||    || |||   |||  | || |||  || |   |  || | | ||   || ||||||||||||||||||||||||||||| ||| |||| ||||| |||||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||
-agagtaagtaatgattctggaatgagggaacttaaatgttgattcttgttggaaatttctcttgatccattgtagctcaccatattttccattgttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcat-tgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
     | | |||   |||     |   |  | |||    |||    || |||   |  |   || | |  || |   |  || | | ||   || ||||||||||||||||||||||||||||| ||| |||| ||||| |||||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||
-agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 19
cttcgtgaattacccttcagtgctttagacaattatcacttgta-agtttttgttcattgattta--atcttttttttttttccctctgttatct--tattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
 ||| |   |||  |||     |  |  | ||| ||       | | ||  |||| |||| | ||   | | | |||||| || ||   ||||||  | ||||||||||||||||| || || |||||||| || || ||||| |||||||| || |||||||| ||||||||||||||||||||||| ||||||||||||||||
-ttctt---ttattctt-gtcacaattaataatgattctggacacacttgatgttgattggtatagggtatctcttttttatctcttcattatctgttcttgcagTTAGAAATGGCCGAAGAGTGTTTAAAACAAGCAATGGATTTGAGTGGGTTATTGCTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 8
-cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatct--tattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
 |||   | | |         | ||  | ||| ||     |  |  || || | | ||   | |  | ||  |      || || | ||||||  | |||||||||||||||||||| || |||||||| || || |  || |||||||| || |||||||| ||||||||||||||||||||||| ||||||||||||||||
tcttgtcgcaattaataatgattctggacacacttgatgttgattggtattgggt-atctctct--ttttcctagcaactcactttattatctgttcttgcagTTAGAAATGGCTGAAGAGTGTTTAAAACACGCAACAGATTTGAGTGGGTTATTGCTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 19
cttcgtgaattacccttcagtgctttagacaattatcacttgta--agtttttgtt-cattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
    |||       |  ||     |  |    |  || | || |   || |||| |     |||||     |   | |||     | | |    | ||  ||| |  ||||||||||||||||  | ||| |||||||||| |||||||||||||| || || ||||||||| | ||||||||||| ||  || |||||||||
---tgtgggagcaacagcaaaatctctgtttctcgtctcctggatttgtctttgatgtggggatttccaactaactctttccgtttttatgtcatcatgacagCTGCAAATGGCTGAGGAATGCATGAAGTATGCGATGGATTTGAGTGGTTTGTTACTTCTTTATTCTTCTCTGGGAGATGCTGAAGGTGTAACAAAACTTG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
----cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
         |||  |  | |  ||   |||    | | ||  ||  ||   |  |  | | | | | | ||| ||   ||| |   | |||| | | ||   || |  || |||| ||||| ||  | ||| | || ||||| |||||||||||||| || || ||||||||||| ||||||||||| ||  | ||||||||||
caatgccaatgagctttcttctagc-ttttgcggattcattgctgatat-ctactacttactaagtgattctcttgcatttgtg--tgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 23
------cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatcttattgc--agTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
       ||  | |  | |  | ||||| | |||   ||| | ||    | |||   | | |    | |  |  ||||  |||| |   |  |  |   | | |  || | || ||||||||||||||  | | |||||| ||||| ||||||||| || ||||||| |||||||| || |||||||| || |||||    || || |
gtgaccattttttagctgcaat-cagtgttctagg--attcttac--aaaggttaaagctaacatgtatttttcttttcattttccttcccatgcttggactacttagCTGGATATGGCTGAGGAATGCATGAGGCATGCTATGGATTTGAGTGGTCTGCTGCTGCTTTATTCTTCATTGGGAGATGCAGATGGAATGATGAAGCTGG

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|110728301|gb|EE103751.1|EE103751
EST:     GTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG                         TTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTG
genomic: GTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAGgtattctgtt ... cttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTG
EST: gi|161716849|gb|FC068107.1|FC068107
EST:     GTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG                         TTAGAAATGGCTGAGGAATGTTTAAAGCATGCAATGGACTTGAGTGGTTTG
genomic: GTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAGgtattctgtt ... cttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgttcattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG
              atttaat  putative branch site (score: 4)
               tttaatcttttttttt  CT-rich tract
     tgttcattgatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - cccttca
- - - - - - - - - - - - - - - - - - cacttgt