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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctaggaaaccaaatttgaatcgtttcattttcttatggttactaatatctgcatacaatctcactgtcactgttcatatggtatcatgttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTGGACGAGCTGAAGTACATGGCTGTTGACATGGGAACTGAAATTGAAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g06860.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G00640.1 (Glycine max), 3'ss of exon 4
---ctgctaggaaaccaaatttgaatcgtttcattttcttatggttactaatatctgcatacaatctcactgtcactgttcatatggtatcatgttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTGGACGAGCTGAAGTACATGGCTGTTGACATGGGAACTGAAATTGAAAG
   ||       |   | | | || ||    || | |   | |     | |||| |      ||| |     | |      | ||   ||  |  | |||||||| ||| |    |||||||||||  |||| |||||||||||| |||| ||||  ||||| ||  |||||||||||||||||||| | || ||||| ||
catctttctcccactaacactagactctagacactgttagacgaca--ttatatttattgttaatattgaattaagctactaaataaaat-gtcctgaaacagGTTGAAAAAAAGAAGCAAGATGATGCACTATCAGATTTAAGTGATCTGTTGGGAGAGCTTAAAGACATGGCTGTTGACATGGGATCCGAGATTGAGAG

upper sequence: Vv17s0000g06860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G08450.1 (Glycine max), 3'ss of exon 4
ctgctaggaaaccaaatttgaatcgtttcattttcttatggtt-actaatatctgcatacaatctcactgtcactgttcatat---------ggtatcatgt--taaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTGGACGAGCTGAAGTACATGGCTGTTGACATGGGAACTGAAATTGAAAG
            |||| || |      || |||||| |   |  |  |   |||    |   | | | | | | | || |  |           ||  ||||  | |||||||| ||  |    |||||||||||  |||| |||||||||||| |||| ||||  ||||| ||   ||||||||||||||||||| | || ||||| ||
------------caaactttatcttcatccttttctcactatccagcagactctagtcattgttttattattaatattgaattcagctactaaataaaatgtcctgaaacagGTTGAGAAAAATAAGCAAGATGATGCACTATCAGATTTAAGTGATCTGTTGGGAGAGCTTAAAGGCATGGCTGTTGACATGGGATCCGAGATTGAGAG

upper sequence: Vv17s0000g06860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G32710.1 (Glycine max), 3'ss of exon 4
ctgctaggaaaccaaatttgaatcgtttcattttcttatg-gttactaata--tctgcatacaatctcactgtcactgttcatatggtatcatgttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTGGACGAGCTGAAGTACATGGCTGTTGACATGGGAACTGAAATTGAAAG
 || ||     |  | | ||| |     | ||  |||||     |||  ||  | |      ||  |     |||        | || || ||  | |||||||| ||| | |  |||||||||||  |||| |||||||||||| |||| ||||  || |||||   ||||||  ||||||||||| |||||||||  ||
-tg-taattttcatattatgattttcacctttgccttatacaacactgttagatttattcttaacgttgaattcagcaactgaaaggaat-atcctgaaacagGTTGAAAAAGGGAAGCAAGATGATGCACTGTCAGATTTAAGTGATCTCTTGGGAGAACTGAAAGGCATGGCCATTGACATGGGATCTGAAATTGGGAG

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|71889052|gb|DT038107.1|DT038107
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|71885181|gb|DT034236.1|DT034236
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|110418340|gb|EC984487.1|EC984487
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|56408671|gb|CX016923.1|CX016923
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|30330505|gb|CD013767.1|CD013767
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|27586846|gb|CB009541.1|CB009541
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|352773351|gb|FQ470938.1|FQ470938
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|110430333|gb|EC996884.1|EC996884
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|110412633|gb|EC978388.1|EC978388
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|32269033|gb|CD718192.1|CD718192
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|32457663|gb|CD798837.1|CD798837
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|110410237|gb|EC975915.1|EC975915
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|71890575|gb|DT039630.1|DT039630
EST:     CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: CTACAAGAACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
EST: gi|71883490|gb|DT032545.1|DT032545
EST:     AACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAG                         GTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG
genomic: AACACCACCTCCTGAACCGACCAATGCACTGCAGAAAGTTGAGgtctgtattt ... gttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatctgcatacaatctcactgtcactgttcatatggtatcatgttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTGGACGAGCTGAAGTACATGGCTGTTGACATGGGAACTGAAATTGAAAG
                                           atgttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctaggaaaccaaatttgaatcgtttcattttcttatggttactaatatctgcatacaatctcactgtcactgttcatatggtatcatgttaaaacagGTGGAACATGCAAAGCAAGATGACACACTTTCAGATTTAAGTAATCTATTGGACGAGCTGAAGTACATGGCTGTTGACATGGGAACTGAAATTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
ctgctag
- - - - aaaccaa
- - - - - - - - - - - - - - - - - cttatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtcactg