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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcttcttgatgcttatagcaatgttcaattctattctctctctcccttctcttgagtttagacccatataataagctgcttcactgtttctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTGTTCATAGGCATTTCATTGCTGGCACCTGATGAGCCAAAAG

Basic information

species Vitis vinifera
transcript Vv14s0068g00780.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G07510.2 (Glycine max), 3'ss of exon 11
----aggcttcttgatgcttatagcaatgttcaattctattctctctctcccttc-tcttgagtttagacccatataataagctgcttcactgtttctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTGTTCATAGGCATTTCATTGCTGGCACCTGATGAGCCAAAAG
     |  |  |  ||| ||  | || |       |  || ||   | |   ||  |  |||||||||     | | ||    | ||| ||  |     ||||||||||||||| |||||||||||||||||||||| || |||||||||| |||||| || |||||||| |||||||||||||||||  ||||||
tttttgtatggtgaatgtttgaatcattacattgatgaatgctgaatatgttttgataatgagtttagg----tgtgatgtaatactt-accttcctgaaagcagGTATTTGATGCATTAAGGACAACAATGTTTATGCTTGGAATGATGTGTGTGTTTATTGGCATTTCTTTGCTGGCACCTGATGAATCAAAAG

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G26550.1 (Glycine max), 3'ss of exon 11
-----aggcttcttgatgcttatagcaatgttcaattctattctctctctcccttc-tcttgagtttagac-ccatataataagctgcttcactgtttctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTGTTCATAGGCATTTCATTGCTGGCACCTGATGAGCCAAAAG
          | |  |||  |  | || |       |  || ||   | |   ||  |  |||||||||     || |||||  || | |  |||      | ||||||||||||| ||||||||||||| ||||||||||| |||||||||| |||||| || |||||||| |||||||||||||||||  ||||||
ttttgtatggtgtgaatgtctgaatcattacattgatgaatgctgaatgtgttttgataatgagtttaggggtgatgtaata--ctaccttcctga-----acgcagGTATTTGATGCATTAAGGACAACGATGTTTATACTTGGAATGATGTGTGTGTTTATTGGCATTTCTTTGCTGGCACCTGATGAATCAAAAG

upper sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------------------------aggcttc---ttgatgcttatagcaatgttcaattctattctctctctccc--ttctcttgagtttagacccatataataagctgcttcactgtttc-tcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTGTTCATAGGCATTTCATTGCTGGCACCTGATGAGCCAAAAG---------
                                               ||||    | || |  ||    ||| | | ||  ||  | |     |    |    || ||||||    |     | || |  ||  ||  ||| | || ||||| || ||| |  |||| ||||||||||| ||| |||||||||||| ||| |||||||||||||| || || |||||||||||  ||| ||         
gttcatctattgactacattgtgatgcttttcctctcttttctttatcttcgggctaatacggatctagatgattagtttgatcattttgtcacagaatggtgtgggtttagggatagtcgcttagataattttcttcttccttaaacagGTTTTCGATGCGCTAAGAACAACAATGTTCATATTAGGAATGATGTGTGTATTCATAGGCATTTCTTTACTAGCACCTGATGATACAAGAGGCAATGAGA

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|351040762|gb|FQ438306.1|FQ438306
EST:     GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAG                         GTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
genomic: GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctc ... tctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
EST: gi|351046211|gb|FQ442589.1|FQ442589
EST:     GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAG                         GTATTTGGTACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
genomic: GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctc ... tctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
EST: gi|351030030|gb|FQ430772.1|FQ430772
EST:     GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAG                         GTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
genomic: GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctc ... tctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
EST: gi|351043780|gb|FQ431332.1|FQ431332
EST:     GGACTTTCTTCTCTATCTGTACAGGATTTGTATACTTTCAGGAATATCAG                         GTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
genomic: GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctc ... tctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
EST: gi|351013510|gb|FQ425541.1|FQ425541
EST:     GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAG                         GTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG
genomic: GGACTTTCTTCTCTATTTGTACAGGATTTGTATACTTTCAGGAATATCAGgtgctctctc ... tctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttctcttgagtttagacccatataataagctgcttcactgtttctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTGTTCATAGGCATTTCATTGCTGGCACCTGATGAGCCAAAAG
                                   cttcactgtttctc  CT-rich tract
                      atataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcttcttgatgcttatagcaatgttcaattctattctctctctcccttctcttgagtttagacccatataataagctgcttcactgtttctcaagcagGTATTTGATACATTAAGGACAACAATGTTTATACTAGGAATGATGTCTGTGTTCATAGGCATTTCATTGCTGGCACCTGATGAGCCAAAAG

- - - - tgatgct
- - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttc