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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctgcccttctctattaaccttttggttgctctacttagcaaaaaaaaaaaaaaaaggttgctcactttaagctacaagttgtttaagtctattctttcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGGGAATCAAAGACAAATATGGCTGTGGTACTTCTGGAAGCTGGACTGGCGA

Basic information

species Vitis vinifera
transcript Vv14s0068g00720.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
gtcctgcccttctctattaaccttttggttgctctacttagcaaaaaaaaaaaaaaaaggttgctcactttaagctacaagttgtttaagtctattctttcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGGGAATCAAAGACAAATATGGCTGTGGTACTTCTGGAAGCTGGACTGGCGA
                           ||    ||  |  |||         ||   |  |   |  |||  |  |  || |  |   |    |||||       |||||| || |||||| |||| |||||||| ||||||||||| || || |||||||| || || || || ||||||   || |||||||| ||||| ||||| |
---------------------------gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattct-------acagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA

upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G07350.1 (Arabidopsis thaliana), 3'ss of exon 12
gtcctgcccttctctattaaccttttggttgctctacttagcaaa-aaaaaaaaaaaaaggttgctcactttaagctacaagttgtttaagtctattctttcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGGGAATCAAAGACAAATATGGCTGTGGTACTTCTGGAAGCTGGACTGGCGA
                           ||    | | |   ||   || ||  ||     ||| |  | | |     |   |||  | |       |  |  | | |||||||||||||||||| || |||||||| || || |||||||||||  | |||||||| | ||||||  |||||   || || || ||||||||  | || |
---------------------------gtaaaccgaatgcacatctaagaattaatctcagtttcctattcttttaaatgggtttctcatactctattataatcacacagATTGAAGTTGAAACCGTGGATAGAACCGGTACTTTCTTGGGATCCATGTGGGAATCGAGGACAAACGTGGCTACAGTTCTGCTTGAAGCTGGCTTAGCAA
















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|110731966|gb|EE106841.1|EE106841
EST:     AGATACTGCAGAGGGATGTTGAG                         ATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
genomic: AGATACTGCAGAGGGATGTTGAGgtcctgccct ... tcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
EST: gi|30304038|gb|CB980832.1|CB980832
EST:     ATGAAGCAATTGCATTGATGAGAAGGAAGATACTGCAGAGGGATGTTGAG                         ATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
genomic: ATGAAGCAATTGCATTGATGAGAAGGAAGATACTGCAGAGGGATGTTGAGgtcctgccct ... tcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
EST: gi|71857364|gb|DT006419.1|DT006419
EST:     ATGAAGCAATTGCATTGATGAGAAGGAAGATACTGCAGAGGGATGTTGAG                         ATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
genomic: ATGAAGCAATTGCATTGATGAGAAGGAAGATACTGCAGAGGGATGTTGAGgtcctgccct ... tcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
EST: gi|30304101|gb|CB980895.1|CB980895
EST:     ATGAAGCAATTGCATTGATGAGAAGGAAGATACTGCAGAGGGATGTTGAG                         ATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG
genomic: ATGAAGCAATTGCATTGATGAGAAGGAAGATACTGCAGAGGGATGTTGAGgtcctgccct ... tcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaggttgctcactttaagctacaagttgtttaagtctattctttcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGGGAATCAAAGACAAATATGGCTGTGGTACTTCTGGAAGCTGGACTGGCGA
       tgctcac  putative branch site (score: 2)
                                    tctattctttcttat  putative PPT
                                      tattctttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctgcccttctctattaaccttttggttgctctacttagcaaaaaaaaaaaaaaaaggttgctcactttaagctacaagttgtttaagtctattctttcttatacagATTGAAGTTGAAACAGTAGATAGAACAGGGACATTCTTGGGATCTTTATGGGAATCAAAGACAAATATGGCTGTGGTACTTCTGGAAGCTGGACTGGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA