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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgctggcaccatttcctgtgcattcctttattttcaataagggcatgtgtcatggctataatcacagatcacttatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC

Basic information

species Vitis vinifera
transcript Vv13s0019g00880.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
tctgctggcaccatttcctgtgcattcctttattttcaataagggcatgtgtcatggcta-taatcacagatcacttatttgattgtttttttctt-tacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
            ||||  ||      |  |  |||| ||    |   | | ||||   |  |  |    | | || | |    || | | |   |  |  ||||||| ||||| || ||||| || ||||| ||||||||||| || ||| | |||||||| || || || || ||||| || ||||||||||| |||||||
----------gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC

upper sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 14
tctgctggcaccatttcctgtgcattcctttattttcaataagggcatgtgtcatggctataatcacagatcacttatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
            ||||||  |   |    |  | ||   |||  |  ||     ||||| || |      |    || | ||      | |  | |  ||||||| || || || ||||| || || |||||||||||||| || ||||| |||||||| ||||| || || |||||||| ||||||||||| |||||||
---------gtaatttccaataagta---tggtgtttgctaacagtttgc----tggctttattttt---ttgggtact-gacatccatgtcatatctagGTTACCACTGTGGACAAGTTCCAGGGCCAGCAAAATGATTTCATTTTACTTTCTCTTGTCCGTACCCGTTTTGTGGGTCATCTTCGTGATGTCAGAAGAC

upper sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 12
----tctgctgg-caccatttcctgtgcattcctttattttcaataagggcatgtgtcatggctataatcacagatcacttatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
    | |  ||| ||  |       |      |  ||||||   | | |   ||  ||     || | | |    |   || | | | || ||  |      |||||||||||||| |||||||||||||||||||||||||||||||| || || |||||||| |||||||| || || |||||||| |||||||| |||||| 
atgatgttttggacagtagagtaaatagccatcaatattttttttgaagttgtgattctcaatta-agttatctctgttttctataaatgattgctct----cagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTCTTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT

upper sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
------tctgctgg-caccatttcctgtgcattcctttattttcaataagggcatgtgtcatggctataatcacagatcact-tatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
      | |  ||| ||  |          | | ||| |||||  | |   |    | |||      | |||   | | ||| ||  |||||| | |        |||||||||||||| |||||||||||||||||||||||||||||||| || || ||| |||| |||||||| || || |||||||| |||||||| |||||| 
gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctct--------cagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT

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|30127856|gb|CB913195.1|CB913195
EST:     TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAG                         GTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
genomic: TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAGgtaaattatt ... ttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
EST: gi|161706722|gb|FC055075.1|FC055075
EST:     TTATCAACAGACGATGTGTTCCATATGATTTCATAGGTCCTCCCAGTAAG                         GTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
genomic: TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAGgtaaattatt ... ttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
EST: gi|110699544|gb|EE076634.1|EE076634
EST:     TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAG                         GTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
genomic: TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAGgtaaattatt ... ttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
EST: gi|30129758|gb|CB915097.1|CB915097
EST:     TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAG                         GTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG
genomic: TTATCAACAGACGATGCGTTCCATATGATTTCATAGGTCCTCCCAGTAAGgtaaattatt ... ttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgtcatggctataatcacagatcacttatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
                               atttgat  putative branch site (score: 5)
                                     ttgtttttttctttac  CT-rich tract
                             ttatttgattgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgctggcaccatttcctgtgcattcctttattttcaataagggcatgtgtcatggctataatcacagatcacttatttgattgtttttttctttacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC

- -gctggca
- - - - - ccatttc
- - - - - - - - - - -gcattcc
- - - - - - - - - - - - - - - - - - -aataagg
- - - - - - - - - - - - - - - - - - - - - - gcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -tcatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaca