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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattacacaattgcttttcaaaccataaattatcgatatcgattcttctggggaatatttaacctgaaaaggtattgcttcaccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAATAAAGCTCTTCTGGAATACAAGGAAGAAGTAACAAATGGTTCATTCCCTG

Basic information

species Vitis vinifera
transcript Vv15s0046g02170.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G61530.1 (Arabidopsis thaliana), 3'ss of exon 4
gttaattacacaattgcttttcaa--accataaattatcg-atatcgattcttc--tggggaatatttaacctgaaaaggtattgcttcaccttctg----cagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAATAAAGCTCTTCTGGAATACAAGGAAGAAGTAACAAATGGTTCATTCCCTG
|| || | |   |    |  |  |  | |||   |  ||   |||  ||  |||  |     ||| ||  |        | ||  ||  |  || |     |||||||| |||||||| |||||   ||| |  |||||||||||||||||||| ||||| ||  |||| || |||||||||||| | ||    |  || || |
gtaaaatcctggaccattcatatatcatcatgcttcttcctgtatttatgattcattatctgatagtttccgctgtgttgcatccctatattttttcatttcagGTTACTCCAAAGTTTTGCAAACAGTACGCTCAAGTAGGAGAAGTGATCAACAAAGCCCTCTTGGAGTATAAGGAAGAAGTATCCAAACACTTGTTTCCAG
















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|34319717|gb|CF372471.1|CF372471
EST:     TAGTTTANCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
EST: gi|110428509|gb|EC994983.1|EC994983
EST:     TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
EST: gi|110428428|gb|EC994900.1|EC994900
EST:     TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
EST: gi|110704726|gb|EE081728.1|EE081728
EST:     TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGGCAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
EST: gi|110704743|gb|EE081769.1|EE081769
EST:     TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGGCAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
EST: gi|71875196|gb|DT024251.1|DT024251
EST:     TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
EST: gi|110373622|gb|EC937874.1|EC937874
EST:     TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAG                         GTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT
genomic: TAGTTTACCATGATCTGCTGGGAATGATGCAACACCCACATCATGCTAAGgttaattaca ... ccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgattcttctggggaatatttaacctgaaaaggtattgcttcaccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAATAAAGCTCTTCTGGAATACAAGGAAGAAGTAACAAATGGTTCATTCCCTG
                   atttaac  putative branch site (score: 3)
                                     ttgcttcaccttct  putative PPT
                aatatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaattacacaattgcttttcaaaccataaattatcgatatcgattcttctggggaatatttaacctgaaaaggtattgcttcaccttctgcagGTTACCCCAAAGTTCTGCAAGAGGTATGGACAAGTAGGAGAAGTGATCAATAAAGCTCTTCTGGAATACAAGGAAGAAGTAACAAATGGTTCATTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT