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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttctctctactgtcttacatcagctttgtaattgtttaatgtctaggtcatggtcatatatattttcctgattttcttgtctcttgttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC

Basic information

species Vitis vinifera
transcript Vv13s0019g02000.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g01910.1 (Oryza sativa), 3'ss of exon 7
------------------------------ctttttctctctact-gtcttacatcagctttgt--aattgtttaatgtctaggtcatggtcatatatattttcctgattttc-ttgtctcttgttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC
                               |||  ||    | | |||   |  ||  ||||   |||  | |||  |  |   | || |  || | |  |    ||  ||   ||          | | ||||  ||||||||||||||||||||||||||||| || ||||| ||||| ||||| |||||||| |||||    ||   ||||||||   | |||||||  |
gtttgcattcttaaaacttatacaaaccaaatttggcttaagatttgtccagctacaagtttgctaaatcttgtaagatggaaagc-tgattttagagacctgatggaagttaactgcgctgcacctgttgcagGTAATGATGAAAGATCAGTTTGCAAACTATGTGGTGCAGAAGGTGCTAGAGACTTGTGATGATCAGCAGAGGGAGGCGATCCTTACAAGGATAAAAGCAC

upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g74030.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------ctttttctctctactgtcttacatcagctttgt------aattgtttaatgtctag---gtcatggtcatatatattttcctgattttcttgtctcttg--ttggattc---agGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC
                                      || |   |  ||| || || || || || ||        |   || |    |||    |  | | | ||     ||      | |  ||||||| ||   ||| | ||   ||| ||||||||||||||| |||||||||||||| |||||||| ||| | ||||| |||||||| |||||    ||  |||||||||   | ||||||| ||
gtttgtgtctgttttaacttgtgggcatatttcgttatttctatgcggtacagttttgcaacatctctgcttctcagaaaattaagcacctaatatgaaaagttgatggtccttgctaaaagtgacttgtctttttgtttgaaatctgaagGTGATGATGAAAGATCAATTTGCAAACTATGTGGTACAGAAGGTGTTAGAGACCTGTGATGATCAGCAGAGAGAGATGATCCTTACAAGGATAAAAGCTC

upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G012964_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------------ctttttctctctactgtcttacat-cagctttgtaattgtttaatgtctaggtcatggtcatatatattttcctgattttc---ttgtctcttgttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC
                                                          |  |   | ||  ||   | |  ||   ||| ||  || || |||  |  |  | | || | |  |  | |  |     |||  |  || | |    |||  ||||||||||| ||||| ||||||||||| || ||||| ||||| || || ||||| || |||||    ||  ||||| | |   | |||||    |
gtatgctgatgctttggtctttttattttcttttaagaatgttttatttaagcagaactgaccaaaatgctttgtttaccactcaataactggctagtggctaatttgtcttgagatctttactgataagatatgggttgcgttgtggttgcgctagGTAATGATGAAAGACCAGTTCGCAAACTATGTGGTGCAGAAGGTGCTAGAAACTTGTGACGATCAGCAGAGGGAGATGATCTTAACAAGGATAAAGACAC

upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 9
ctttttctctctactgtcttacatcagctttgtaattgtttaatgtctaggtcatggtca-tatatattttcctgattttcttgtctcttgttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC
   ||| |  ||   |    |  | |  | ||| || | | |||| ||   |  |   |  |||   | |   |    |  |  ||  |  |  ||| ||||| ||||||||||| |||||||||||||| || || ||||| ||| |||| || ||||||||    ||||  || ||| | ||   ||| ||    ||||
ggatttgtacctgtggaggaagctgatttgtgttat-ggtgaatgcctcaattgtttccggtatgcgtatgagtagcctgatgttcggtgatgtgatgcagGCAATGATGAAAGACCAGTTTGCAAACTACGTGGTCCAGAAGGTGTTGGAAACCTGTGATGAATCTCAACGCGAGCTGTTGCTGGGTCGTATTCGGGTTC

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|32459731|gb|CD800905.1|CD800905
EST:     TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAG                         GCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
genomic: TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAGgtttgtcagt ... ttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
EST: gi|34363480|gb|CF405065.1|CF405065
EST:     TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAG-CTCTTCAG                         GCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
genomic: TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAGgtttgtcagt ... ttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
EST: gi|110700862|gb|EE077890.1|EE077890
EST:     TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAG                         GCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
genomic: TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAGgtttgtcagt ... ttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
EST: gi|30126410|gb|CB911749.1|CB911749
EST:     TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAG                         GCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
genomic: TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAGgtttgtcagt ... ttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
EST: gi|30131767|gb|CB917106.1|CB917106
EST:     TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAG                         GCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
genomic: TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAGgtttgtcagt ... ttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
EST: gi|30301304|gb|CB978098.1|CB978098
EST:     TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAG                         GCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG
genomic: TCCTGGTGAATGAGATGCTTGGCTCCACTGATGAAAACGAGCCTCTTCAGgtttgtcagt ... ttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaggtcatggtcatatatattttcctgattttcttgtctcttgttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC
                        tcctgat  putative branch site (score: 3)
                              ttttcttgtctcttgt  CT-rich tract
            tcatatatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttctctctactgtcttacatcagctttgtaattgtttaatgtctaggtcatggtcatatatattttcctgattttcttgtctcttgttggattcagGCGATGATGAAAGATCAGTTTGCAAACTATGTTGTACAGAAAGTGCTGGAGACATGTGATGACCAGCAACTTGAACTGATCCTTAATCGAATAAAAGTTC

- - - - - -tactgtc
- - - - - - - - - - -catcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - catggtc