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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaatttgtttctgtttccttcaatttcttagcaatcaaacagggagatgaaagaatggattagggttcaaaagaatttaacagctaccttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGTGGAGGGAAGAGACTACAAATTGGTTTGGAACCTATGCAATGAGGTTTGA

Basic information

species Vitis vinifera
transcript Vv03s0038g01960.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G00680.1 (Glycine max), 3'ss of exon 1
-aagaatttgtttctgtttccttcaatttcttagcaatcaaacagggagatgaaagaatggattagggttcaaaagaatttaacagctaccttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGTGGAGGGAAGAGACTACAAATTGGTTTGGAACCTATGCAATGAGGTTTGA
 | ||| ||      | || |     |   | ||     |||    |    |  | |||  |      || |     ||    |  ||  |||   | ||||   ||| || ||  || | |||||  |||||||||||||||| |||||||  || ||||| || ||||| |||||||||| |||| |||||||||| ||
aatgaagtttgaaaagattacaggtgtcattaagatgataaatgatgcttggtcacaatccacatttttttattgccatgctccttcttgcttga-tacagGTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGTCAAGAGAAGAAACAACAAACTGGTTTGGAAGCTATACAATGAGGTTCGA
















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|37187961|gb|CF607312.1|CF607312
EST:     CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATG                         GAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGT
genomic: CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATGgtatgatcct ... ttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGT
EST: gi|110731604|gb|EE106171.1|EE106171
EST:     CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATG                         GAATAAAGGTTACCATGGCATGTGCCAACACTAATGGACAAATCACAATGT
genomic: CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATGgtatgatcct ... ttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGT
EST: gi|37188651|gb|CF608000.1|CF608000
EST:     CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATG                         GAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGT
genomic: CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATGgtatgatcct ... ttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGT
EST: gi|110730197|gb|EE107001.1|EE107001
EST:     CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATG                         GAATAAAGGTTACCATGGCATGTGCCAACACTAATGGACAAATCACAATGT
genomic: CGACCAATGCAAGGATGGACAGAGATCCCTCTTCGATTATCCCCTCTATGgtatgatcct ... ttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatgaaagaatggattagggttcaaaagaatttaacagctaccttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGTGGAGGGAAGAGACTACAAATTGGTTTGGAACCTATGCAATGAGGTTTGA
                               atttaac  putative branch site (score: 3)
                                        ctaccttttct  putative PPT
                      ttcaaaagaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaatttgtttctgtttccttcaatttcttagcaatcaaacagggagatgaaagaatggattagggttcaaaagaatttaacagctaccttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGTGGAGGGAAGAGACTACAAATTGGTTTGGAACCTATGCAATGAGGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - ccttcaa
- - - - - - - - - - - - - - - - gcaatca
- - - - - - - - - - - - - - - - - - - - - - - - - gaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagctac