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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgctgagttctccatgtccatccccgcttgacctcattcagagttctacctgcatttcttattttaaatttaacttcttggttctttttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCATGTAATCTCTCTGATCTCATAAATTTAGTTTGAAGTGTCTATTGATTTA

Basic information

species Vitis vinifera
transcript Vv09s0002g02500.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 17
tgtttgctgagttctccatgtccatccccgcttgacctcattcagagttctacctgcatttcttattttaaatttaacttcttggttctttttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCAT-GTAAT-CTCTCTGATCTCATAAATTTAGTTTGAAGTGTCTATTGATTTA
          ||     || | |||     ||  || | |    ||        || |||  | |    || | |||  | ||| |||| |      ||||||||||||| ||||| ||||||||| ||||||| || ||    |||   || | ||| |        || || |  | | ||       | | |  | |  
----------gtgagtaatatacata---actaaacattagcttgaacatgttatg-attcatgaac--aactctaagctgttgcttctctaaa---cagGCGACTGGCACATGGCTTACATTTGCCTGTACAAAGCTCGTGTTATCTGAATTGGAATGCCAGACAGGCTGATGAGCTGATTTGTTTACATTTCTCAAGT--
















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|30296415|gb|CB973209.1|CB973209
EST:     TAATCCAATCCCCCAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCCCCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|33404879|gb|CF210506.1|CF210506
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GTGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|110422111|gb|EC988423.1|EC988423
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|22009658|gb|BQ794692.1|BQ794692
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTCGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|33405442|gb|CF211069.1|CF211069
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGC
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGC
EST: gi|110701778|gb|EE079734.1|EE079734
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAAGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|22008798|gb|BQ793832.1|BQ793832
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|83275868|gb|DV939876.1|DV939876
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GTGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|71879968|gb|DT029023.1|DT029023
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|22009589|gb|BQ794623.1|BQ794623
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|22012121|gb|BQ797155.1|BQ797155
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|110428084|gb|EC994545.1|EC994545
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAGCTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|22009862|gb|BQ794896.1|BQ794896
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|83275368|gb|DV939376.1|DV939376
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
EST: gi|22010204|gb|BQ795238.1|BQ795238
EST:     TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAG                         GCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA
genomic: TAATCCAATCCCACAGCGAGAGGAAGACATCACTAAACTGTCTGGAGGAGgtaagatcac ... tttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctacctgcatttcttattttaaatttaacttcttggttctttttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCATGTAATCTCTCTGATCTCATAAATTTAGTTTGAAGTGTCTATTGATTTA
                          atttaac  putative branch site (score: 3)
                                cttcttggttcttttt  CT-rich tract
            atttcttattttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgctgagttctccatgtccatccccgcttgacctcattcagagttctacctgcatttcttattttaaatttaacttcttggttctttttgtttcagGCGACTGGCATATGGCATACATTTGCATGTACAAGGCCCGCACCATCCCCATGTAATCTCTCTGATCTCATAAATTTAGTTTGAAGTGTCTATTGATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
tgtttgc
- - - - - - -ctccatg
- - - - - - - - - - -ccatccc
- - - - - - - - - - - - - - - - tgacctc
- - - - - - - - - - - - - - - - - - - - - - - - - tacctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttgg