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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatttttgagattccccaaaaaggatcacatgtcttttcagtgggtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G17010.2 (Glycine max), 3'ss of exon 8
acatttttgagattccccaaaaaggatcacatgtcttttcagtgg-gtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG
|  | ||    ||  |      |      |  ||  |    | |   ||   || || |     | | |  | |  |||     || |  | |  |  ||||||||||| |||||||| ||||||||  | ||||| | ||| || |||||||| |||||||| || |||||||| |||||||||||||| ||||||
atctcttatcaatcacaattttattgcttctagtaatcatggcgctataaattcttttacatatacgcttatgatgtttgtgt-ttattttctgttcccagACAAGTGCATCTTTGAAATTCACAGTATTAAACCCAATGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATCTATGCTGATACG

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 8
-acatttttgagattccccaaaaaggatcacatgtcttttcagtgggtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG
   |    ||  ||     |   |       |||   |   | |   |      | |  | |   || || | || ||      || |    |  |||||||||||||| || || || ||||||||  ||||||| ||||| || |||||||| |||||||| || |||||||| |||||||| ||||| ||||||
ctaacagctgtcatcagtaatgtattgatgaatgcaataatactat-tgcttatagttgtaattttgataattaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 8
acatttttgagattccccaa-aaaggatcacatgtcttttcagtgggtatcctcat--tcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG
    |      | ||  ||  || | ||   |   |     | |     | || ||  |  | |   || || | || ||      || |    |  |||||||||||||| || || || ||||||||  ||||||| ||||| || |||||||| |||||||| || |||||||| ||||| |||||||| ||||||
---ctaacagcagtcatcagtaatgtattgaagaacgcaataatactattgcttatagttgtaattttgatacttaatttgtttgtttatttactatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 7
acatttttgagattccccaaaaaggatcacatg-tcttttcagtgggtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG
   || || |   |      |  |  ||   |  || |     |    || ||  | ||| |  |  |||| |   ||      ||||  | |  |  ||||||||||| |||||||| ||||||||  | ||||| | ||| || |||||||| ||||| || || |||||||| ||||| |||||||| ||||||
ctcttattaatcataattttattgcttctagtaatcatggtgctataaattcttttacataaacac-ttatgatgtttgtttgtttgttttctgttcccagACAAGTGCATCTTTGAAATTCACAGTATTAAACCCAATGGGCCGAATTTGGACAATGGTTGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG

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|110363218|gb|EC926793.1|EC926793
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|71882514|gb|DT031569.1|DT031569
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGTTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|111125104|gb|EE253722.1|EE253722
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|32247604|gb|CD713423.1|CD713423
EST:     ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|351054175|gb|FQ450257.1|FQ450257
EST:     GAAGAGTTATGAGTCCTACAGAAACCCTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|71888760|gb|DT037815.1|DT037815
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|30325227|gb|CD008489.1|CD008489
EST:     ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|110698225|gb|EE075525.1|EE075525
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|349820930|gb|FQ408638.1|FQ408638
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|110702653|gb|EE078810.1|EE078810
EST:     CTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: CTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|32271862|gb|CD721021.1|CD721021
EST:     ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|351035742|gb|FQ463587.1|FQ463587
EST:     GAAGAGTTATGAGTCCTACAGAAACCCTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|32271741|gb|CD720900.1|CD720900
EST:     ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|349822202|gb|FQ412466.1|FQ412466
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|110416323|gb|EC982295.1|EC982295
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|111125102|gb|EE253720.1|EE253720
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|32272154|gb|CD721313.1|CD721313
EST:     ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: ATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|71882170|gb|DT031225.1|DT031225
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGTTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|161718453|gb|FC065040.1|FC065040
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
EST: gi|351044803|gb|FQ449057.1|FQ449057
EST:     GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAG                         ACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG
genomic: GAAGAGTTATGAGTCCTACAGAAACCTTTATTCATGGGCTAGATGAAAAGgtacatatgg ... attcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG
                                            tattctt  CT-rich tract
                  atgttattaaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatttttgagattccccaaaaaggatcacatgtcttttcagtgggtatcctcattcatgaggatgttattaaactttacaagttgtcatattcttgcagACAAGTGCCTCTTTGAAGTTCACAGTTCTGAACCCCAAGGGACGGATTTGGACTATGGTAGCAGGAGGAGGTGCAAGTGTCATCTATGCAGATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - ttcccca
- - - - - - - - - -aaaagga
- - - - - - - - - - - - - - acatgtc