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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggccaccgcaacagagtccttttatccctctatttggattcccttaaaaatatgggaaaatattcacttttgctttaataattaacgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAGCTGAGCGAGGCGATGGAATGTTTGGAGCATATATGCACAGAAGGGTGCA

Basic information

species Vitis vinifera
transcript Vv17s0000g09790.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G36500.1 (Glycine max), 3'ss of exon 3
gtaaggccaccgcaacagagtccttttatccctctatttggattcccttaaaaatatgggaaaatattcacttttgctttaataattaacgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAGCTGAGCGAGGCGATGGAATGTTTGGAGCATATATGCACAGAAGGGTGCA
                        || ||  |  | ||| ||||   |||   ||    ||  |  |  |  ||    | | |||||| | |    |||||||||| | |    |||  | | ||||||||   | | |||||  |||||||||||||||||||||| ||||||||||| |||||||| || ||||| |
--------------------gtaattaataacattgttttgattatattagtgattaatgagga-gtgaaaattaa--taattaattagcttgg--cagAGGAAGAGGAGGGTGAGGAAGTGGAGGGAGGAGGAGAGGTTGTACGTGCAGCTGAGCGAGGCGATGGAGTGTTTGGAGCACATATGCACGGAGGGGTGTA

upper sequence: Vv17s0000g09790.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G13540.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------------gtaaggccaccgc-aacagagtccttttatccct--ctatttggattcccttaaaaatatgggaaaatattcacttttgctttaataattaacgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAGCTGAGCGAGGCGATGGAATGTTTGGAGCATATATGCACAGAAGGGTGCA
                                                                                               | | |     |||  |   |||  |   | |  |  | | |||  |    ||||  |||    ||       | | ||||||   || | |  ||   ||||||||| |||  |   ||| ||  ||||  ||||  | |  | ||   | ||||||||||||||||||| |||||||| || ||||||   || |||||||
gtaattaactaatcaacacaatcaattaattaattttcaaactgagtgaatttttcttagtccaagatcagagattaattttgtttgctcgcgatgcatgatggtcgctgatcaagttttgcaaacattaccaaattgagtgaaattaattataattaaactgtagtagtattgcttatttattgattgtttgacagAGGAAAAAGAAATCGAGGAGGTATAGGATGGAACAGGGGATATACGCGGAGCTGAGCGAGGCGATGGAGTGTTTGGAACACATATGCTATGAGGGGTGCA
















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|161717443|gb|FC067556.1|FC067556
EST:     ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAGAAGCGAAGCAGGCGGCGTAGGGAGGAAAGGTGTTTGTATATGCAG
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAG
EST: gi|34550620|gb|CF518838.1|CF518838
EST:     ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATATGCAG
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAG
EST: gi|34548181|gb|CF516413.1|CF516413
EST:     ACCCC-ATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAGAAGCGAAGCAGGCGGCGTAGGGAGGAAAGGTGTTTGTATATGCAG
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAG
EST: gi|34550534|gb|CF518752.1|CF518752
EST:     ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATATGCAG
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAG
EST: gi|161718052|gb|FC067587.1|FC067587
EST:     ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAGAAGCGA
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGA
EST: gi|161714279|gb|FC064170.1|FC064170
EST:     ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAGAAGCGAAG
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGAAG
EST: gi|110700643|gb|EE077475.1|EE077475
EST:     ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCG                         AGGAAAAAGCGAAGCAGGCGGCGTAAGGAGGAAAGGTGTTTGTATATGCAN
genomic: ACCCCCATCTCGAGCTCGAGATTATGCAGTTCATGGAAGAATCTGAATCGgtaaggccac ... cgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttaaaaatatgggaaaatattcacttttgctttaataattaacgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAGCTGAGCGAGGCGATGGAATGTTTGGAGCATATATGCACAGAAGGGTGCA
                                       aattaac  putative branch site (score: 2)
                aaaatattcacttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggccaccgcaacagagtccttttatccctctatttggattcccttaaaaatatgggaaaatattcacttttgctttaataattaacgtaaaacagAGGAAGAAGCGAAGTAGGCGGCGTAGGGAGGAAAGGTGTTTGTATCTGCAGCTGAGCGAGGCGATGGAATGTTTGGAGCATATATGCACAGAAGGGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA