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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcaatgtagctacactgcacttctgttgatatcacgaataaaatgcacattttacttgtatttagatgtggcctgtggagaattagctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC

Basic information

species Vitis vinifera
transcript Vv18s0001g12750.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G03290.1 (Glycine max), 3'ss of exon 7
gttagtgcaatgtagctacactgcacttctgttgatatcacgaataaaatgcacattttacttgtatttagatgtggcctgtggagaattagctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC
                                     |      |           |    | || ||      | |    || | |||||  |   | |   |   || ||  |||||          | |   |||  ||  |||||| | | |||  | ||||| |||||  |||||||||| ||||| || |||||||||||||| |||||| ||||||||||||||||  | || |||||  
-------------------------------------ttgtcgttcggcccttgtgtcaggtagtgttgtagcataggtgctgaaaaattaattagttacaaataactacttaaagtaa----------gctttttttgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGAGCAGGGGACCTTTTTGCAAGTGGATTTTTGTATGGAGTGGTCAAGGGTT

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G07980.2 (Glycine max), 3'ss of exon 7
gttagtgcaatgtagctacactgcacttctgttgatatcacgaataaaatgcacattttacttgtatttagatgtggcctgtggagaattagctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC
                             ||   | || ||   | | |   |  |  |  || | || |  ||    |     |  ||   ||  | ||| ||  ||||| ||| | |  | || || ||            |||||| |  || ||  | || || || || ||||||||||||||||| || || |||||||| || |||||| ||||||||||||||||  |  | || || |
-----------------------------tgaaaa-attacttttgagacaaaagtact--tttttttcaactgcaaacca---aatatgtacta-actctagtcattattatgaattatgtttgaaacgtg-----------tcagATTGCACGTGTCCCGGCAATTGGAGAAGCAAAGGCAACTGATGCAACAGGGGCAGGGGATCTTTTTGCAAGTGGATTTTTGTATGGAGTGATCAAAGGTC

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G37040.1 (Glycine max), 3'ss of exon 7
gttagtgcaatgtagctacactgcacttctgttgatatcacgaataaaatgcacattttacttgtatttagatgtggcctgtggagaattagctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC-
                                       |||| || ||          |      |||||   ||   | |  | |   |     | |   ||  ||| | |||        ||          |   | | |||||| |  || ||  | |||||||| || || ||||||| |||||| || || |||||||| || |||||| ||||||||||||||||  |  | || || | 
--------------------------------------tacgagtagaaaagctcccaaaaggacttttagccttg---tatccaaagagactctaacttcagtcattactatgaactgtgcttgc-------tttaaatgtatcagaTTGCACGGGTCCCGGCCATAGGCGAAGCCAAGGCAATTGATGCAACAGGGGCAGGGGATCTTTTTGCAAGTGGATTTTTGTATGGAGTGATCAAAGGTCT

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|71874454|gb|DT023509.1|DT023509
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|110717578|gb|EE093555.1|EE093555
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|30129522|gb|CB914861.1|CB914861
EST:     AAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: AAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|110697937|gb|EE075379.1|EE075379
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|45770865|gb|CN006717.1|CN006717
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|30304551|gb|CB981345.1|CB981345
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|46918792|gb|CN548121.1|CN548121
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|110697939|gb|EE075381.1|EE075381
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|33401764|gb|CF207391.1|CF207391
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGTGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|33401843|gb|CF207470.1|CF207470
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGTGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|45368254|gb|CK906613.1|CK906613
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGTGGAAGAGAG                         ATGCTCCGAGTCGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|352769558|gb|FQ468486.1|FQ468486
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|110732830|gb|EE108461.1|EE108461
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|110697936|gb|EE075378.1|EE075378
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|30125766|gb|CB911105.1|CB911105
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|352769709|gb|FQ468637.1|FQ468637
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|32459727|gb|CD800901.1|CD800901
EST:     GTGGTGACGCTAGGTTCTAATGGTTGCCCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: GTGGTGACGCTAGGTTCTAATGGTTG--CCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
EST: gi|110429129|gb|EC995617.1|EC995617
EST:     CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAG                         ATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA
genomic: CAGTGGTGACGCTAGGTTCTAATGGTTGCCTTGCAAAATGCGGAAGAGAGgttagtgcaa ... tttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC
                     gagtaac  putative branch site (score: 2)
                                      ttacctttttatttc  putative PPT
                                      ttacctttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgcaatgtagctacactgcacttctgttgatatcacgaataaaatgcacattttacttgtatttagatgtggcctgtggagaattagctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA