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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatttatttatttatttttctgagcttagttttgttgctatgagatccatttgaggtgtcttcgttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG

Basic information

species Vitis vinifera
transcript Vv15s0048g00370.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g19740.1 (Oryza sativa), 3'ss of exon 1
--------tttatttatttattta-tttttctgagcttagttttgttgctatgagatccatttgaggtgtcttcgttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG
          | ||||||| |||| |   |  ||  ||| | ||||| |  | |  ||| | | |  | | ||  ||   | |   |  |  ||||     ||  ||        ||  |||||  |||||| || |||||||||| ||| ||||||||||||||||| || || |||||||||||||||||||||||||
tgaattatcatctttatttgtttagtcagtaagatattaatattgtt-ccgttaattccttcttaattttttttattagaggatcatatttgtttgtgcagATGGAT--------GATCTGAAAGCTTTCCGGCAGTGGGGAAGCAGAACTCCTGGTCACCCAGAAAACTTCGAAACACCTGGTGTTGAAGTCACTACTG

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 1
----tttatttatttat--ttatttttctgagcttagttttgttgctatgagatccatttgaggtgtcttcgttcctga-aattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG
    |  | | ||||||  | |||| | || |  || |  |  |  | |  | |    ||    ||  |    |  ||| ||   ||| |  |||          ||   || ||  |||||| |||||| |||||| |||||| ||| ||||||||||||||||||||||| |||||||| ||||||||||| || |
tctttccaatcatttatgctcatttctatgtgactattcctccttttgtcgggtgatctttctctgcttataattttgataaccatgtttactggc-------gcagATGGACGATCTGAAAACTTTCCGACAATGGAGAAGCAGAACTCCTGGTCACCCAGAAAATTTTGAAACACCTGGCGTTGAAGTCACCACAG

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------------------------------------tttatttatttatttatttttctgagctt-agttttgttgctatgagatccatttgaggtgtcttcgttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG
                                                                                             |  | ||||  | ||||||     ||| || |||     | |   | | | || || |       || |||||    |||   |    |   ||| ||||| ||||| ||||| || ||||||||||||||||| |  || || || || || || ||||||||||| ||||||||||||| ||||||||
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagat-------ttgctgaagcagtgt---tgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------tttatttatttatttatttttctgagcttagttttgttgctatgagatccatttgaggtgtcttcg--------ttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG
                                             || ||  || || | | |||  ||     | |     || | ||| || ||| ||| |  |  | |        |  ||||||    |||||| |  |   ||| ||||| ||||| |||||    |||||||||||||||||||  ||||| || || || || ||||| ||||| |||||  |||||||||||||||
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaag--gtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG

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|110689991|gb|EE066698.1|EE066698
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|351013311|gb|FQ425016.1|FQ425016
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|161705830|gb|FC057107.1|FC057107
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|71860244|gb|DT009299.1|DT009299
EST:     GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGA
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGA
EST: gi|110689389|gb|EE065571.1|EE065571
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|110687702|gb|EE065414.1|EE065414
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|110700650|gb|EE077489.1|EE077489
EST:     GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|110686000|gb|EE063214.1|EE063214
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|71863785|gb|DT012840.1|DT012840
EST:     GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTG
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTG
EST: gi|77579456|gb|DV218569.1|DV218569
EST:     GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|161713434|gb|FC063712.1|FC063712
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
EST: gi|34548489|gb|CF516721.1|CF516721
EST:     GCATGCTTCAGTATGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGG                         GAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC
genomic: GCATGCTTCAGTACGCTCTGCTTCACCTTGCTGGCTACGACAGTGTCAGGgtttgtgcat ... gaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatccatttgaggtgtcttcgttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG
                           aaattttgtgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatttatttatttatttttctgagcttagttttgttgctatgagatccatttgaggtgtcttcgttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -ctatgag
- - - - - - - - - - - - - - - - - - - - - - - - ccatttg