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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG

Basic information

species Vitis vinifera
transcript Vv14s0066g01060.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgt-taactcataat---gcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                                                || | | |   |  |  || ||||      || |     | ||  ||| ||    ||   ||   |||   |||| | ||| |  |  |     ||  | |||| || ||||| || || || || |||||||||   ||||||    ||||||||||||||||||||||||| |||||||||||||||||||| |||||  |
--------------------------------------------------------------------------------aaacttcaagagtactgaactatgaagctatcttt-tgcagttactcaacaaaagcagaaaaa--catagttaacatgtaatttttggtcgaatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagt-tcatcagta-acgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                                                || | | |   |  |  || ||||      || |     | ||  ||| ||    ||   ||   |  | |  |    ||   |  |  |  ||  | |||| || ||||| || || || || |||||||||   ||||||    ||||||||||||||||||||||||| |||||||||||||||||||| |||||  |
--------------------------------------------------------------------------------aaacttcaagagtactgaactatgaagctatcttt-tgcagttactcaacaaaagcagaaaaacatagttaacatgtattttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g50260.1 (Oryza sativa), 3'ss of exon 3
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatt-tttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                                ||| |  |  || |||||| |  |       ||  | || || | ||  || | || | | ||    |     |||| |       |||||  ||  |||    ||     | |||| || || ||||| || || |||||||| |||    | |||  | |||| |||||||| |||||||| || ||||| ||||||||||| |||||||| ||
---------------------------------------------------------------ttcagtgctcacttgtagaaaccgacaggattcaggactaagggaaag--ctaaaaacactagt----acaagtatctga-------agtaatatttgctctctgtga----tgcagGCGATGATTGTGTTTCCATCCAGACAGGCTGCAGTGACATAAACATACATAATGTGAACTGTGGACCAGGGCATGGGATCAGCATTGGTGGTCTAGGAAG

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 5
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                            |  || |    |||  ||  |||   |  || |  | | |||    ||||| | |  ||||      |    ||  | |||          |||| ||   |  |  |      | |||| || || ||  | || || ||||||||||||   || |||    ||||||| |||||||||||||| || |||||||||||||| || || |||||  |
------------------------------------------------------------cctgtaaaccctgcatgtcaaaggacatgtttc--agagtta----agagtacactgaaaa------actgctgtaaactagc-------ataacattcctttgtcctattcgatgcagGTGATGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACACAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G00230.1 (Glycine max), 3'ss of exon 4
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                                      | | || ||  |   ||| ||  ||| | |  |    ||   || |  || |||||||  |     || |       | |||||  || |||| || |  ||| | |||| || || || || || ||||| || || |||||  | ||||  ||||||||||||||||||||||||||||||||||||||||||||| |||| || ||
--------------------------------------------------------------------aatgggtattatgaa-ataatttaagcagagtagt--ttgaacactga--aacttggtcaata-----atttgttcatgtgagtaaaatttactc-tactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G08730.1 (Glycine max), 3'ss of exon 4
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                                    |||||  || | |     || ||  |||      |   |     | | ||||  ||||||  |     || |      || ||| |  ||   |  || |  ||  | |||| || |||||| | || ||||| || || |||||  | ||||  ||||||||||| |||||||| ||||| |||||||||||||||||| |||| || ||
--------------------------------------------------------------------ttttgaaag-aaatcaacaaattaagcagggaagtatgaa----cactcaaacgtggtcaata-----atttgttcatatgagttaaatttgtt-gtactaaatcgtgcagGTGATGACTGTATCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTGGAAGTCTTGGAAG

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G08710.1 (Glycine max), 3'ss of exon 6
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtc-atttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                          |   |||| |  ||  | | | |     ||| | |    | | |     | | |  ||| | | |    ||| ||    | | ||    || |  || |  || |  | ||  || | |  ||       |  | |   ||||          |||  | ||||  ||||||||||| |||||||| ||||| ||||||||||||||||             
-------------------------------------------------------ggtgatgggtccaccttctcaacttgtttattaattagtcacataatccaatataattttcaaatact--accatgatatgaaaccaacaaaataaaaaaagAGAAATAGTGATA-ATACAATGGGGATACTTTTCGCAATGATACT---------CTCGGACATATATGTACACAATGTCAATTGTGGGCCTGGCCATGGAATCAGCATTG-------------

upper sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G14650.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatca-gtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                                                                                   | |   |||| ||   ||  | |    |     ||| |  ||     || | | ||    || || |  | |||||||||||||| |||||| ||||||| || || |||||||| |||||   | ||||| ||||  | ||||| ||||| |||||||| ||||||||||| || || | 
--------------------------------------------------------------------------------------------------gtaaccacagactct--acttattgaagctatgatgaaacttaccacgatgaagaaataacaattcct--ttcattctacagGAGATGACTGTATATCAATTCAAACGGGATGCTCGAATATCAACATACACGATGTAGACTGTGGCCCTGGCCATGGAATTAGCATTGGAGGACTGGGAAA

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|161706245|gb|FC055437.1|FC055437
EST:     CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTG                         GAGACGACTGTGTATCAATACAGACAGGATGC
genomic: CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTGgtaaatccaa ... cattctacagGAGACGACTGTGTATCAATACAGACAGGATGC
EST: gi|110371123|gb|EC934902.1|EC934902
EST:     CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTG                         GAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACA
genomic: CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTGgtaaatccaa ... cattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACA
EST: gi|110381463|gb|EC934529.1|EC934529
EST:     CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTG                         GAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACA
genomic: CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTGgtaaatccaa ... cattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACA
EST: gi|110363249|gb|EC926825.1|EC926825
EST:     CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTG                         GAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACA
genomic: CCTACAGAACTCCCAAAATGTGGTGATCTATAGCACAAATCTAGCTTGTGgtaaatccaa ... cattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG
                                     tcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG