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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctctttgtaagtgcaaatgggtgggaaatatcttacccttctctctttgaccaagaattttttaatttggttgatatttatcggttaaaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA

Basic information

species Vitis vinifera
transcript Vv08s0007g00530.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G39930.1 (Glycine max), 3'ss of exon 1
-actctctttgtaagtgcaaatgggtgggaaatatcttacccttctctctttgaccaagaattttttaat-ttggttgatatttatcggttaaaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA-
 |  |||  |  ||   || |||  |  |       |  |     |    | ||       |||||||    |   ||| |  |  || |     |||||||| ||||||||||| || ||||| || |||||| || |||| | ||| || |||||| |||| |||||||| || |||||  |||| ||||| |  || || 
aatgctcaattcaataccatatgcatttgtgggtggtagctgacttaggatagataccatgttttttatcactaactgagaactggcgtt---gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAGAGGTCTGGTTAGAACAGATGAAAGCAAACAGAACATTGGTGCTGCAGAT

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G39930.2 (Glycine max), 3'ss of exon 1
--actctctttgtaagtgcaaatgggtgggaaatatcttacccttctctctttgaccaagaattttttaat-ttggttgatatttatcggttaaaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA
  |  |||  |  ||   || |||  |  |       |  |     |    | ||       |||||||    |   ||| |  |  || |     |||||||| ||||||||||| || ||||| || |||||| || |||| | ||| || |||||| |||| |||||||| || |||||  |||| ||||| |  || ||
caatgctcaattcaataccatatgcatttgtgggtggtagctgacttaggatagataccatgttttttatcactaactgagaactggcgtt---gcttttcagGACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAGAGGTCTGGTTAGAACAGATGAAAGCAAACAGAACATTGGTGCTGCAGA

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G37660.1 (Arabidopsis thaliana), 3'ss of exon 1
actctctttgtaagtgcaaatgggtgggaaatatcttacccttctctctttgaccaagaattttttaatttggt--------tgatatttatcggttaaaatttt--cagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA
                               |    |  | || |||||   |    | ||| |  ||||   |        || |   ||| | |    | | |  |||| ||||| || ||||||||||||||||||||| | || ||||| || || || ||||| || || ||| ||||||| |||||||| ||    ||||  ||
------------------------------gttctctctctttatctctacaatgtggtattgtgaaattccataagaacactgttcaatattgatggtgactgtgacagGACAAATTGTGTATAAGAAATTGAAGGAGAGGTCGGAGCAGTTCGTGGCAAGGGGTTTAGTGAGGACAAAGGAGAGTAAGGAGAAGATCAATGGAGAGGA

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|349811666|gb|FQ409663.1|FQ409663
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|349810529|gb|FQ402772.1|FQ402772
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCTGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|351016336|gb|FQ446196.1|FQ446196
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|349821239|gb|FQ404371.1|FQ404371
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|110700744|gb|EE077667.1|EE077667
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|110385557|gb|EC950093.1|EC950093
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|352786365|gb|FQ478974.1|FQ478974
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCGGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|351023663|gb|FQ448214.1|FQ448214
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|352790186|gb|FQ481385.1|FQ481385
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCGGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|351051751|gb|FQ449565.1|FQ449565
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|351054211|gb|FQ450293.1|FQ450293
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|351028714|gb|FQ433144.1|FQ433144
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|110692043|gb|EE070833.1|EE070833
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
EST: gi|351055225|gb|FQ440564.1|FQ440564
EST:     AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAG                         GCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA
genomic: AATGGCGGATTTGCCCACAGTTCTTGTTACCGGTGCCGGCGGTAGAACAGgtacaccggt ... aaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttgaccaagaattttttaatttggttgatatttatcggttaaaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA
                                                ttttc  CT-rich tract
          aagaattttttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctctttgtaagtgcaaatgggtgggaaatatcttacccttctctctttgaccaagaattttttaatttggttgatatttatcggttaaaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - -gcaaatg
- - - - - - - - - - - - - ggaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttga