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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattgctcaattactttgactgttgtagattactgaagttctagttctaggttagagatcaattccttattaactcttctgttttggtattttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTTTTCAAGCAACAGAAGAGGGGTTTATCTCTCTTGTTGCTAGACAGTGGTC

Basic information

species Vitis vinifera
transcript Vv03s0038g02650.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G42910.1 (Glycine max), 3'ss of exon 2
ctattgctcaattactttgactgttgtagattactgaagttctagttctaggttagagatcaattcc--ttattaactcttctgttttggtatttttta---cagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTTTTCAAGCAACAGAAGAGGGGTTTATCTCTCTTGTTGCTAGACAGTGGTC
   |   |||  || ||  |||  |||     ||  |  ||   |  |    |||  ||  |||     ||  |||   |  | |||   ||||||  |   |||| |||||||||||||| ||||| |||||   ||||||||| ||||||||  | ||||||||||||||||||||||| ||  | ||||| |||||||  ||
---tccttcatgtattt--acttgtgttttgaacccatttttctgcacattattatcgaataatgaaaattgataaacatattctttctctattttaaatgtcagGATTTACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCACTCCAAGCAACAGAAGAGGGGTTTATTTCAGTGGTTGCCAGACAGTTTTC

upper sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G24100.1 (Glycine max), 3'ss of exon 2
ctattgctcaattactttgactgttgtagattactgaagttctagttctaggttagagatcaattccttattaactcttctgttttggtatttt---ttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTTTTCAAGCAACAGAAGAGGGGTTTATCTCTCTTGTTGCTAGACAGTGGTC
  |||  |  ||    | |  |||| |  |  | |    | |   |  |    |  | |   | |  | |||||   |  | |||   ||||||   || |||| || ||||||||||| ||||| |||||   ||||||||| ||||||||  | ||||||||||||||||||||||| ||  | ||||| |||||||  ||
-cattcatggatgtactcg--tgttttgaaccatttttctgcacatgatttactgcataatgaatgttgattaaacatattctttctctattttaaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCACTCCAAGCAACAGAAGAGGGGTTTATTTCGGTGGTTGCCAGACAGTTTTC
















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|110699119|gb|EE075838.1|EE075838
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|71864084|gb|DT013139.1|DT013139
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|71862550|gb|DT011605.1|DT011605
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|71864104|gb|DT013159.1|DT013159
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|110684850|gb|EE062597.1|EE062597
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|110684787|gb|EE062462.1|EE062462
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|294966370|gb|GW839477.1|GW839477
EST:     GGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: GGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|156737705|gb|EV241826.1|EV241826
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|110730859|gb|EE108423.1|EE108423
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCANCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|110699744|gb|EE077009.1|EE077009
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|110699328|gb|EE076229.1|EE076229
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
EST: gi|71864275|gb|DT013330.1|DT013330
EST:     ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGA                         GGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT
genomic: ACCCGAGACGGCCCGGTACATCAATGATCACCTCTTCCATCATCTCAAGAgtaagttact ... ttttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaggttagagatcaattccttattaactcttctgttttggtattttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTTTTCAAGCAACAGAAGAGGGGTTTATCTCTCTTGTTGCTAGACAGTGGTC
                       tattaac  putative branch site (score: 1)
                                           tatttttt  putative PPT
                                     ttttggtatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattgctcaattactttgactgttgtagattactgaagttctagttctaggttagagatcaattccttattaactcttctgttttggtattttttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTTTTCAAGCAACAGAAGAGGGGTTTATCTCTCTTGTTGCTAGACAGTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
ctattgc
- - - - - - - - -tgactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caattcc