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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctttggtgataactgtggtatgaagttttttgttgggtaattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG

Basic information

species Vitis vinifera
transcript Vv04s0023g00670.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 1
tcctttggtgataactgtggtatgaagttttttgttggg-taattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG
    ||  |  |     |  |||  |  |     |||   | ||| |    ||||| |||  ||||   | | |     || |||  |||  |||||||||||||||||||||||||||||| ||
-ttattattatttttactcatatctatataaagattgaaatcattattgcttttttttttctttttcggtcactaatcctgattttattttttttttgcagCTCGAAGGAGAGACCCACTCTTGG

upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 1
-tcctttggtgataactgtggtatgaagttttttgttgggtaattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG
 |       | || | | |      ||  | | |   |  | |   |   ||| || |||  |||   ||      |    | || ||||  | |||||||||||||||||||||||||||| | 
attaaaatcttattattttttctcaaatctatataaagattgaaattattattgtttttttttttctttttcggtcactaatcttgtttttttatttgcaGCTCGAAGGAGAGACCCACTCTTG-

upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ06557 (Selaginella moellendorffii), 3'ss of exon 1
tcctttggtgata-actgtggtatgaagttttttgttgggtaattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG
       |||| |  |     ||||       ||| | |     ||     | |   | | |   |   |  |||||| |   |  | |    ||||||||| | ||||||||||||||||||||
-------gtgagatgcgaccctatgggccaaattgcttgtcggatccagtgtctaggtctcagaat--ctggttctaatt-cgtgttgtgtgcttttgcagCACCAAGGAGAGACCCACTCTCGG

upper sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ31357 (Selaginella moellendorffii), 3'ss of exon 1
tcctttggtgata-actgtggtatgaagttttttgttgggtaattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG
       |||| |  |     ||||       ||| | |     ||     | |   | | |   |   |  |||||| |   |  | |    ||||||||| | ||||||||||||||||||||
-------gtgagatgcgaccctatgggccaaattgcttgccggatccagtgtctaggtctcagaat--ctggttctaatt-cgtgttgtgtgcttttgcagCACCAAGGAGAGACCCACTCTCGG

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|161720192|gb|FC065495.1|FC065495
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110721235|gb|EE098001.1|EE098001
EST:     CCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: CCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351054991|gb|FQ440330.1|FQ440330
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351032388|gb|FQ461641.1|FQ461641
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110723113|gb|EE100055.1|EE100055
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110689930|gb|EE066595.1|EE066595
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|71880968|gb|DT030023.1|DT030023
EST:     CTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: CTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351023466|gb|FQ432849.1|FQ432849
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351026516|gb|FQ428528.1|FQ428528
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|349810775|gb|FQ403018.1|FQ403018
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|161712997|gb|FC062419.1|FC062419
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|33407242|gb|CF212869.1|CF212869
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110688940|gb|EE068068.1|EE068068
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|349812603|gb|FQ407222.1|FQ407222
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110688724|gb|EE067604.1|EE067604
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110731965|gb|EE106840.1|EE106840
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351016921|gb|FQ424348.1|FQ424348
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|349813885|gb|FQ414119.1|FQ414119
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|30129349|gb|CB914688.1|CB914688
EST:     CTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: CTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|349814805|gb|FQ410028.1|FQ410028
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110700927|gb|EE078011.1|EE078011
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351013638|gb|FQ429779.1|FQ429779
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|349827877|gb|FQ422745.1|FQ422745
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110729615|gb|EE105755.1|EE105755
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110685192|gb|EE063331.1|EE063331
EST:     TCTCACCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGACACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|351046957|gb|FQ454567.1|FQ454567
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|71870540|gb|DT019595.1|DT019595
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110699539|gb|EE076636.1|EE076636
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|349811233|gb|FQ406221.1|FQ406221
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110689548|gb|EE065870.1|EE065870
EST:     ATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: ATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|110724605|gb|EE100577.1|EE100577
EST:     AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: AGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG
EST: gi|33404953|gb|CF210580.1|CF210580
EST:     TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAG                         CTCGAAGGAGAGACCCACTCTCGG
genomic: TCTCAGCCTCACCTCTCCTTCGATCCCTCTTCGGTCTTGGTTTATGAGgttctcttct ... atttttgcagCTCGAAGGAGAGACCCACTCTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG
                    gattaat  putative branch site (score: 3)
                                 tgttttcttttcattt  putative PPT
     tttttatttaattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctttggtgataactgtggtatgaagttttttgttgggtaattctgaaatttttatttaattttgattaattctaagtgttttcttttcatttttgcagCTCGAAGGAGAGACCCACTCTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - -tggtgat
- - - - - - - - - ggtatga
- - - - - - - - - - - - - - - - tgttggg