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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaaacgtttgagacacatgcaccatctatggtttttctactttgctacttcatatattatggcatgtttctgtgtatgggctaatattgaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGACAATGTATCTGCTGGAGGGAAAAGTGAAGGTTTACTGTGATGGGCATGAT

Basic information

species Vitis vinifera
transcript Vv18s0089g01220.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g01220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G33070.1 (Glycine max), 3'ss of exon 1
gtcaaacgtttgagacacatgcaccatctatggtttttc--tactttgcta-cttcatatattatggcatgtttctgtgtatgggctaatattgaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGACAATGTATCTGCTGGAGGGAAAAGTGAAGGTTTACTGTGATGGGCATGAT
   ||  | ||  |     |||    | |   ||  ||   | || ||||| | |  ||||||      | | | ||   |   |  | ||   | |||||||||||| | |   ||||| |||| | |||||| | ||| |||   ||||||| ||||||||||||||||||||||||| ||||     ||| |||  || |
--gaagtgctttggttgtttgcttgctttgaagtgctttggttctatgctatccttttatatttcatactatctttg-acacaagggactaaacattgaacagGTGGGAAGGTGGTCCAACCAAAATTCCATGGTCCTTTAAAGAAGAAGAGACTATGTATCTGCTGGAGGGAAAAGTGAGGGTTACTGTTGAAGGGTCTGTT

upper sequence: Vv18s0089g01220.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G28240.1 (Glycine max), 3'ss of exon 1
gtcaaacgtttgagacacatgcaccatctatggtttttctactttgcta-cttcatatattatggcatgtttctg-tgtatgggctaatattgaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGACAATGTATCTGCTGGAGGGAAAAGTGAAGGTTTACTGTGATGGGCATGAT
      | | |  |         |  | ||  | |||  | || ||||| | |  ||||||      | | | ||    |||||   | |   | |||||||||||| | |   ||||  |||| | |||||| | ||| |||   ||||||| ||||||||||||||||||||||||| ||||     ||| |||  || |
tcttttcttcttggttttgcttgctttgtagtgctttggttctatgctatccttttatatttcatactatctttgacacatgggactaaac--attgaacagGTGGGAAGGTGGTCCAGCCAAAATTCCATGGTCCTTTAAAGAAGAAGAGACTATGTATCTGCTGGAGGGAAAAGTGAGGGTTACTGTTGAAGGGTCTGTT
















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|110714515|gb|EE091508.1|EE091508
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|26264967|gb|CA816030.1|CA816030
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|34320897|gb|CF373651.1|CF373651
EST:     AACCCTCCTCAGGCCACACTCNCCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110421115|gb|EC987403.1|EC987403
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|71872251|gb|DT021306.1|DT021306
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|71890491|gb|DT039546.1|DT039546
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110384464|gb|EC948903.1|EC948903
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110691317|gb|EE069283.1|EE069283
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|26267201|gb|CA818264.1|CA818264
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|77586329|gb|DV222271.1|DV222271
EST:     GATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: GATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|71865417|gb|DT014472.1|DT014472
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110686569|gb|EE064353.1|EE064353
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110393051|gb|EC957895.1|EC957895
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110409568|gb|EC975234.1|EC975234
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|71866736|gb|DT015791.1|DT015791
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110421538|gb|EC987836.1|EC987836
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|30297574|gb|CB974368.1|CB974368
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
EST: gi|110727169|gb|EE103625.1|EE103625
EST:     AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAA                         GTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC
genomic: AACCCTCCTCAGGCCACACTCACCGATCTGGGTGTCACTTCTTGGAAAAAgtaacaccct ... gaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacttcatatattatggcatgtttctgtgtatgggctaatattgaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGACAATGTATCTGCTGGAGGGAAAAGTGAAGGTTTACTGTGATGGGCATGAT
                                   ggctaat  putative branch site (score: 3)
                                      taatattgaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaacgtttgagacacatgcaccatctatggtttttctactttgctacttcatatattatggcatgtttctgtgtatgggctaatattgaatgaacagGTGGGGATGCTCTCCAAGCAAATTCCCATGGACATTTGAAGCTAAAGAGACAATGTATCTGCTGGAGGGAAAAGTGAAGGTTTACTGTGATGGGCATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - acacatg
- - - - - - - - - - -caccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgg