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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatttttctttgttatctggtatgatcatgcttgggtgtaaagtttctggttttctgacatctctctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAACTAAGAGAAATGATGCAAAATCCAGAATTTCTTCGTCAGTTGACTTCAC

Basic information

species Vitis vinifera
transcript Vv04s0210g00220.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0210g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G057158_T01 (Zea mays), 3'ss of exon 3
--------------gtaccatttttctttgttatctggtat-gatcatgcttgggtgtaaagtttctggtt----ttctgacatctctctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAACTAAGAGAAATGATGCAAAATCCAGAATTTCTTCGTCAGTTGACTTCAC
               |||  || || |    ||  || ||  || |||  ||   |||   | || ||  |    |||||| | ||   |  || ||| | |||  | | |||||  |  | |||| | |  | || |||||| ||||| | ||||||||||| || |||||||||||| |||| |||||||| || |
gtatgatgcctgaaatacttttgttgtgaaatacttgataaagagcatatttct-tgtcctgcttatgcataaagttctgataccttgttgatg-cagCTGCTTAATATGAATCCAAATGTACGTAACATGATGGAATCCAATACTCAAATGAGAGAAATGATTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTC

upper sequence: Vv04s0210g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G127101_T01 (Zea mays), 3'ss of exon 3
---------gtaccatttttctttgttatctggtatgat-catgcttgggtgtaaagtttctggttt----tctgacatctctctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAACTAAGAGAAATGATGCAAAATCCAGAATTTCTTCGTCAGTTGACTTCAC
          |    |  || |    ||| || ||  |  |||  ||   |||      | |         ||||| | | |  |  || ||| | |||  | | |||||  |  | |||| | |  | || |||||| ||||| | |||||||||||  | ||||||||||||||||| ||||| || || |
gtatgatgcttgaagtacttgtgaaatatttgataaaaagcatattttcttgtccctgctatacacccgagtctgatacccccttgatg-cagCTGCTTAATATGAATCCAAATGTACGTAACATGATGGAATCCAATACTCAAATGAGAGAAATGATTGAGAATCCAGAATTTCTTCGCCAGTTAACATCTC
















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|71877103|gb|DT026158.1|DT026158
EST:     TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAG                         ATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
genomic: TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAGgtaccatttt ... ctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
EST: gi|110695633|gb|EE073874.1|EE073874
EST:     TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAG                         ATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
genomic: TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAGgtaccatttt ... ctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
EST: gi|30135176|gb|CB920514.1|CB920514
EST:     TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAG                         ATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
genomic: TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAGgtaccatttt ... ctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
EST: gi|111125152|gb|EE253737.1|EE253737
EST:     TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAATATATGAACCAG                         ATACTTGGTNTCAATCCCCAGTTGNGTAGCGTTCTTGATTCCAATCCTCAA
genomic: TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAGgtaccatttt ... ctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
EST: gi|110385709|gb|EC950257.1|EC950257
EST:     TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAG                         ATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA
genomic: TATCACAGATGATGCAGAGCCTCCTTTCCAGTCCTCAGTATATGAACCAGgtaccatttt ... ctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatcatgcttgggtgtaaagtttctggttttctgacatctctctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAACTAAGAGAAATGATGCAAAATCCAGAATTTCTTCGTCAGTTGACTTCAC
                                ttctgac  putative branch site (score: 2)
                                        tctctctatt  CT-rich tract
                  taaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccatttttctttgttatctggtatgatcatgcttgggtgtaaagtttctggttttctgacatctctctattgtcagATACTTGGTCTCAATCCCCAGTTGCGTAGCGTTCTTGATTCCAATCCTCAACTAAGAGAAATGATGCAAAATCCAGAATTTCTTCGTCAGTTGACTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA