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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctcccattctattagtaagagatcttactggcatctgtgcaatatttattgtgcaccaatcggatattgcttatggtccttgtatcttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCTCTGCAGACACTTAAGACTGAGGAAAGAAAAGTGGATGTTGATAAAGAGT

Basic information

species Vitis vinifera
transcript Vv15s0021g01420.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g01420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G26100.1 (Glycine max), 3'ss of exon 4
---aaatctcccattctattagtaagagatcttactggcatctgtgcaatatttattgtgc-accaatcggatattgctta-tggtccttgtatcttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCTCTGCAGACACTTAAGACTGAGGAAAGAAAAGTGGATGTTGATAAAGAGT
      |   ||||  |  |  ||   | | ||  | | |  |     |||||   | ||| |    ||    |||||| |  ||   ||  |   |||   |||||||||||||| || ||||||||||||||||||||||| |  |||||||| |||||| | |  || ||||| | |||||| |||||  |  |  ||    
tattcttgctccatcatgcttttagtgggttttgtttgaaattt----atattctctatgctattgttcacccattgctaaacggaatttaaactgtgttg-tagGAGATGACACTGGAAGAGTATGAGAAGGTGCTGGAAGAGAAAAGGAAGGCCCTGCAGGCTCAAAAAACTGAAGCAAGAAAGGTGGACATCAAGGAATTTG

upper sequence: Vv15s0021g01420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G13900.1 (Glycine max), 3'ss of exon 4
------aaatctcccattctattagtaagagatcttactggcatctgtgcaatatttattgtgcaccaatcggatattgcttatggtccttgtatcttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCTCTGCAGACACTTAAGACTGAGGAAAGAAAAGTGGATGTTGATAAAGAGT---
        ||    ||| || |||||  |  || ||  ||  || | |      | | | |   |    ||     ||||| |  |   ||  | ||  |   |||||||||||||| || ||||||||||||||||||||||| |  || ||||| |||||| |||  || ||||| | |||||| |||||  |    || ||||   
ttgctcgtatgcggcatgcttttagtgggttatgtt--tgaaatttatat----tctctaggttattgttcatcctttgctaaatggaatttaaactgttttgtagGAGATGACACTGGAAGAGTATGAGAAGGTGCTGGAAGAGAAAAGAAAGGCCCTGCAGGCACAAAAAACTGAAGTAAGAAAGGTGGACATC---AAGGAGTTTG

upper sequence: Vv15s0021g01420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G39080.1 (Glycine max), 3'ss of exon 4
aaatctcccatt-ctatta--gtaagagatcttactggcatctgtgcaatatttattgtgcaccaatcggatattgcttatggtccttgtatcttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCTCTGCAGACACTTAAGACTGAGGAAAGAAAAGTGGATGTTGATAAAGAGT---
    ||   ||| |||||   ||| |        || |    ||       ||| ||        || |  || |  | ||  |  || |  ||  |  |||||||||||| || ||||| ||||| || || || ||||| || ||||||||| ||||  |||||||||||||||| ||||| || |||  |   ||||  |   
--gccttttatttctattgttgtatgtagaaaccctagtgaatgcttttagtttgtttaaattttattgcttaatagt-attttttttttccctgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCTTTGCAAGCACTTAAGACTGAGGAGAGAAAGGTAGATACT---AAAGTTTTTG

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|352781493|gb|FQ468337.1|FQ468337
EST:     ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|110730185|gb|EE106973.1|EE106973
EST:     ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|110685474|gb|EE062226.1|EE062226
EST:     ACAAGGAGAATCCTGTGAATGAACTTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|28969693|gb|CB348726.1|CB348726
EST:     ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|30327847|gb|CD011109.1|CD011109
EST:     GAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: GAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|71874798|gb|DT023853.1|DT023853
EST:     ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|352773015|gb|FQ470630.1|FQ470630
EST:     ACAGGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|29782926|gb|CB348647.2|CB348647
EST:     ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|32269416|gb|CD718575.1|CD718575
EST:     GAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: GAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
EST: gi|110703187|gb|EE079813.1|EE079813
EST:     ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAG                         GAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT
genomic: ACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggct ... ttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttattgtgcaccaatcggatattgcttatggtccttgtatcttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCTCTGCAGACACTTAAGACTGAGGAAAGAAAAGTGGATGTTGATAAAGAGT
                                             ttgtaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatctcccattctattagtaagagatcttactggcatctgtgcaatatttattgtgcaccaatcggatattgcttatggtccttgtatcttgtaaatagGAGATGACACTTGAGGAGTATGAGAAGGTGCTGGAAGAAAGGAGGAAGGCTCTGCAGACACTTAAGACTGAGGAAAGAAAAGTGGATGTTGATAAAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- -tctccca
- - - - - - - - - -taagaga
- - - - - - - - - - - - - -cttactg
- - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg