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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctacaatatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT

Basic information

species Vitis vinifera
transcript Vv10s0116g01480.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 8
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctacaatatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
                                                                                          |   ||   |  |  ||      |  || |      | ||  |   | ||| | |  |       |||| |  |||   ||    |||||||| || ||| ||||  | ||||| ||| ||||||  |||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||| ||
------------------------------------------------------------------------------------------gtaagatcaactttcatcatcaataggttgcacagatttttttttttacaggtacaagc------atatctttaaccattttaatttgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g31040.1 (Oryza sativa), 3'ss of exon 7
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctaca-atatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
                                                               ||||    | |||    |||||  ||  ||      | |  |||  |       |  | |||| |||  ||   |    || ||  | | || | |||| |     || |  | ||||||| || ||| ||||  | ||||| ||| | ||||  |||||||| |||||||| ||||||||||||||||| |  ||||||||||||||||| ||
---------------------------------------------------------------gtaaggcca-tatccatcacttagttacagtac---atcatgataagat----atactatgttacttcatattcttgactcttgcggttgcatacattttgtcaccat-caaaatgcagGTGCCAATGCCAAGGCTTAGGAAGCGTATCGCAAATCGTTTGAAGGATTCTCAGAACACTTTTGCAATGCTAATTACATTCAATGAAGTTGACAT

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 8
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctaca-atatttggaacttattct--tattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
                                                                                                          |  ||         ||  |||   ||  ||||||||| ||| ||    | ||      |  |||   |  |||||||||| || ||| ||||  | ||||| ||| ||||||  ||| | || |||||||| ||||| |||||||||||||  ||||| ||||||||||| ||
---------------------------------------------------------------------------------------------------------gtaaggccgatactatccattt---acagagttcagatgctgttgaaggatatgcacatattttaccatgatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctacaatatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
                      | |   ||||| || |  |  ||||| ||         |||| ||||||  || ||  |   |||   |    |   || | | | |      | |     | ||   | | |  | |       ||| ||  | || |   |         | |||||||||| ||||||||| |  ||||||| ||||||||| | |||||||| |||||||| ||||| ||  ||||||| || |||||||||||||||||
---------------------gtatgc-aaaatctatcatttttcctggcttccg-----tctg-aaaatttttaaatgactgatcagaggttaaataaagttagtttgttacctaataaaaagctttacagtcacataa----tcagtgatatgacatctaacaac-------actgcagGTTCCGATGACAAGACTTCGGAAACGAGTTGCAACAAGATTGAAAGACTCTCAAAATACTTTCGCGTTGCTGACAACTTTCAATGAAGTTGATAT

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctacaatatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
                                                     || |    || |   |||  |||  |  |||| || | | |    | | ||  |      |||  |    |  | ||||   ||||| |    | |   |  ||||     |  ||   |   |||||||||||||||||||| |  | ||||| || |||||  | |||||||| ||||| |||||||||||  ||||||| || |||||||||||||||||
----------------------------------------------------gtatgaaaactatgtcatt--tattctttactt-atataatgctccgtg-tgttttctctatgaaagaaaagcattttac---gttcacaa---gatttgatgatatc----atctaacatcgatgcagGTTCCTATGACAAGACTTCGCAAACGGGTGGCAACTAGGTTGAAAGACTCTCAGAACACTTTTGCGTTGCTGACAACTTTCAATGAAGTTGATAT

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S154_6V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaagcatcatgaacttaattatttattaaaatatacc-tgtaatcctgtctgttaggggttctgt-aaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctgg-tgctacaatatttggaacttattctta--ttgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
                ||| |  || | | |  ||| |   |    | || ||   |      |||  |  |||   | ||    |    |  |     |  ||  | |||| ||  | |   | |||| ||     | | ||| | ||| || ||   || |       | || ||   || ||||| || |||||  || || | ||  | || || ||||| |||||||||||||| |||||||||||| || ||||||| ||||| ||  |||| ||
---------------gtaagtccttgtgacatcataacacatgcaaccgtttggatgtatgcatgtcgaggttatctttttatggtggtctaaacctgcgctgcctgttgggagtgtattta-cagtttattgt--ggcttagaacttggatgttagggtaatcaacgtctctttttcgttttcagGTACCAATGACCCGACTACGAAAGAGAGTGGCCACACGGTTGAAAGATTCTCAGAACACTTTTGCATTGTTGACCACCTTCAACGAGATTGACAT

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|34548183|gb|CF516415.1|CF516415
EST:     GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGA                         GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
genomic: GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGAgtaagcatca ... cttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
EST: gi|71864219|gb|DT013274.1|DT013274
EST:     GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGA                         GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
genomic: GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGAgtaagcatca ... cttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
EST: gi|71861201|gb|DT010256.1|DT010256
EST:     GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGA                         GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
genomic: GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGAgtaagcatca ... cttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
EST: gi|71868220|gb|DT017275.1|DT017275
EST:     GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGA                         GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
genomic: GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGAgtaagcatca ... cttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
EST: gi|37189774|gb|CF609123.1|CF609123
EST:     GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGG                         GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
genomic: GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGAgtaagcatca ... cttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
EST: gi|110729049|gb|EE105210.1|EE105210
EST:     GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGA                         GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT
genomic: GACCTTCAGCTACAGAACCTGTGCTTCCTCCCAAGGAGAGGGAAAGAAGAgtaagcatca ... cttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttactaagttcagatcctggtgctacaatatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
 ttcttac  putative branch site (score: 2)
                                       cttattctt  putative PPT
                                     aacttattcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctacaatatttggaacttattcttattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG