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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaattttaaaatgtggagttcccaacagcaagagctctttctatatggtgattttttatcctcatgttgcttacctttacaaggatcaatttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA

Basic information

species Vitis vinifera
transcript Vv10s0405g00020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 2
---aagaattttaaaatgt-----ggagttcccaacagcaagagctctttctatatggt---gattttttatcctcatgttgcttacct-ttacaaggatcaatttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA
      || ||||   |||     |  | |  | |  | |   |   |   | ||  ||    |||  |  |  | |  | ||| || | ||  || |   |  | ||||||||| | |||||||| |||||||| |||||||| ||||||||||| ||||||  |||||   |  |||| ||||| ||  | ||||| ||||  |||||| 
gtatgcaactttattttgtttttggtggattgcgatggtactggtgatacatgtactgttcttattgctactgtttagatggctaacttattttaatggatatatcttgcagACCAGGAAAGATGCAACTCAAGTTGTTGCAAACTTGCAAAGGCAGCAAGTCTCCTCAAAAATAGTTGCATCTGAGTATCTAGAAGCAAATAAAGATCTTT

upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G12220.1 (Glycine max), 3'ss of exon 2
aagaattttaaaatgtggagttcccaacagcaagagctctttctatatggtgattttttatcctcatgttgcttacctttacaaggatca--atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA
|  |||   ||  || |   |       | ||   | |  || |  ||| ||   |   ||  |  |  |  ||           ||  |     ||||||| || | ||||||||||||||||| ||||||||||| ||||||||||| || || |  | ||||||||| ||||||||| ||||    ||||| |||||||
agaaataagaatctgggtgatcagtggaatcacatgtttattttg-atgctgtactgcgattgtt-tactatttggtaacctggagactatgggctttgcagGCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTA

upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G01370.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------aagaattttaaaatgtggagttcccaacagcaagagctctttctatatggtgattttttatcctcatgttgcttacctttacaaggatca--atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA
                                                                                     ||||| |   ||    || | |      |   | |  | | | |  ||| ||   |   ||  |  |  |  ||           ||  |     ||||||| || | ||||||||||||||||| ||||||||||| ||||||||||| || || |  | ||||||||| ||||||||| ||||    ||||| |||||||
gtagtaaagaaatttatgatagacctcctgatatttgcactgtttgatgctgttagataccctttgtaggattggtatgcttattaagaaataagaatctgggtgatgtgtggaatcacatgtttattttgatgctgtactgcaattgtt-tactatttggtaacttggagactatgggctttgcagGCCAGAAAAGATGCCACTCAAGTTGTTGCAAATTTACAAAGGCAACAGGTTCAGTTTAAGTTGATTGCATCTGATTACCTGGAGAAAAATATGGATCTTA

upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 2
aagaattttaaaatgtggagttcccaacagcaagagctctttctatatggtgattttttatcctcatgttgcttacctttacaaggatcaatttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA
        ||| || |     |||  | || ||   |    | | |  | | |  ||  ||  |    ||||  |   |        |   |||    ||||  | |||||||| || ||||| ||||||||| | || |||||||| ||  | ||| ||||||||||||||||||| || ||||| || |||||||| |
-------gtaacattt----ctccgtataggaaagacatcatttttgagat-acattggatgattgaattgcgaaaaatctgtcctttttttttaattagACGAGGAAAGATGCTACACAAGTTGTTGCAAATCTACAGAGGCAACAGGTTAATTCACGGTTGATTGCTTCTGATTATTTAGAAGCCAACATTGATCTCA

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|71862887|gb|DT011942.1|DT011942
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGT
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGT
EST: gi|110709185|gb|EE084422.1|EE084422
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|110718449|gb|EE095298.1|EE095298
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|161720393|gb|FC070185.1|FC070185
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|161714917|gb|FC064539.1|FC064539
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|161715770|gb|FC066174.1|FC066174
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|110712226|gb|EE089603.1|EE089603
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|33403466|gb|CF209093.1|CF209093
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|110722059|gb|EE097960.1|EE097960
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|110699863|gb|EE077248.1|EE077248
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|110712662|gb|EE087902.1|EE087902
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
EST: gi|110696026|gb|EE074715.1|EE074715
EST:     AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAG                         ACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC
genomic: AAAATACACTGCGACTTTTAATCACTTGTCTGCCCAAATTAAACTTGGAGgtacatggac ... atttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtgattttttatcctcatgttgcttacctttacaaggatcaatttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA
                        tgcttac  putative branch site (score: 2)
                                              tttttgc  putative PPT
     tgattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaattttaaaatgtggagttcccaacagcaagagctctttctatatggtgattttttatcctcatgttgcttacctttacaaggatcaatttttgcagACCCGCAAAGATGCCACTCAAGTAGTTGCAAATTTGCAAAGGCAACAAGTCCACTCAAGGTTGATTGCTTCTGATTACTTGGAAGCTAATATTGATCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - taaaatg
- - - - - - - - - - - cccaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaagga