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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtacatgacatacttgatttcctatacagtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG

Basic information

species Vitis vinifera
transcript Vv12s0059g01400.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g05020.1 (Oryza sativa), 3'ss of exon 2
ttgtacatgacatacttgatttcctatacagtgaaggaaatatt-gtgatttgaaatg---atatttaatgctacaaatttgatatctgaaa----ttttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
       |  | | ||||  |||||      |||      | ||  | | |||  ||    || || |          |||| ||    |||    | |||| | |||||||| ||||||||||| || || |||| ||||||||| || ||||||||||| || |
------gttgcttccttg--ttcctgcgacctgagatgcttcttcataaattgtcattttcatgttcaggaactaggttttggtactgaaaatagatgttgcttgcagGAGCCCTTTGTGAACATACCTGAAGATAGAATCCGTGAGGCTCTAAAAGTTGTGCTAG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G086418_T01 (Zea mays), 3'ss of exon 2
--------ttgtacatgacatacttgatttcctatacagtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
        |  | |  |  |   ||| |||  | | ||   || ||||| || |         ||    ||| |  |  |  ||||||| |||||||        ||||| || ||||||||||| ||||| |||| |||||||||||| ||| ||||  | || |
aaacatcatgttgctagttaattttgctttgttttccatgaaatgaaatctt-tctcacatcttgtagcttagttttggacttttgata-ctgaaataa------cagGAACCATTTGTGAACATACCAGAAGATAGAATCCGTGAAGCTCTAGAAGTCATCCTAG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G086418_T02 (Zea mays), 3'ss of exon 2
-----------------------------------------ttgtacatgacatacttgatttcctatacagtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
                                         |  | |  |  |   ||| |||  | | ||   || ||||| || |         ||    ||| |  |  |  ||||||| |||||||        ||||| || ||||||||||| ||||| |||| |||||||||||| ||| ||||  | || |
atatgatataattgaccactattccttctatcaaaacatcatgttgctagttaattttgctttgttttccatgaaatgaaatctt-tctcacatcttgtagCTTAGTTTTGGACTTTTGATA-CTGAAATAA------CAGGAACCATTTGTGAACATACCAGAAGATAGAATCCGTGAAGCTCTAGAAGTCATCCTAG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G086418_T03 (Zea mays), 3'ss of exon 2
ttgtacatgacatacttgatttcctatacagtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
            | |||  ||| | ||  | ||||     | |      ||| |       ||| |  |  |  ||||||| |||||||        ||||| || ||||||||||| ||||| |||| |||||||||||| ||| ||||  | || |
----------tttgctttgttttccatgaaatgaaatctttctcacatcttgtagc-----ttagttttggacttttgata-ctgaaataa------caggaaccatttgtgaacataccagAAGATAGAATCCGTGAAGCTCTAGAAGTCATCCTAG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G43550.1 (Glycine max), 3'ss of exon 2
-----ttgtacatgacata-cttgatttc--ctatacagtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
      |||  ||||   | ||||||||    | ||   | |   | | | ||| |  | |  ||| || |    ||  ||  |||  |     | || ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||
acaaagtgtg-atgatggaacttgattttaattttatgttaagaaagaaagtgttagataacctgaaatctt---ctttaaccttgtgac----acttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAAAAGTTGTTCTTG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 2
-----ttgtacatgacatacttgatttcctataca-gtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattt-tgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
       ||   |     |||||||||    |  | ||  || ||  |      ||| | || |  || |||  |     ||     | ||||| || ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||| ||||||||||||
acaaagggtgattatggaacttgattttaattttatgttcagaaagca----agttttagataaccttaaatcttct---ttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG

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|30256135|gb|CB971978.1|CB971978
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|110389980|gb|EC954860.1|EC954860
EST:     GTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: GTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|351015527|gb|FQ447356.1|FQ447356
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|26258262|gb|CA809325.1|CA809325
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|26257485|gb|CA808548.1|CA808548
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|351045015|gb|FQ449269.1|FQ449269
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|71857429|gb|DT006484.1|DT006484
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|110379464|gb|EC944660.1|EC944660
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|30253155|gb|CB970706.1|CB970706
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCCCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|351022573|gb|FQ447095.1|FQ447095
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|351034099|gb|FQ448017.1|FQ448017
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|110362858|gb|EC926416.1|EC926416
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|29785487|gb|CB342539.2|CB342539
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|30253078|gb|CB970629.1|CB970629
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCACTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|30256204|gb|CB972047.1|CB972047
EST:     TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: TCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
EST: gi|83275093|gb|DV939189.1|DV939189
EST:     CAAGTCGAAT-GGATTAAGC-TTTTCAGTTTGGAA-TGNAAGGATATAAG                         GAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT
genomic: CAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTG-AAGGATATAAGgtatattttc ... ttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG
                          aaatttgatatctgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtacatgacatacttgatttcctatacagtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattttgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - acatgac
- - - - - - - - - - - - - - - - - -ggaaata
- - - - - - - - - - - - - - - - - - - - - - - - - -gaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgctac