Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatacatgcacataggcttgttttatgattcttccatgaaaatatgttcaatgccctgaatttttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACTTATTATGTTGCCAGAAGCAATTTCTAAAAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02540.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 6
gtaatatacatgcacataggcttgttttatgattcttccatgaaa----atatgttcaatgccctgaatttttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACTTATTATGTTGCCAGAAGCAATTTCTAAAAG
|||||||| ||   |   ||  | || |    || | |||| | |       ||||  |     | ||||  ||||| || ||| ||||||| |||||||| || || ||||||||||||  |||||||||||| |||||||| || |||||||||  |||
gtaatatatatttgctctggagt-ttctggatttttgccataatatgtggagtgtttcactaattcaattaatcatgtagACGTCTGCCAAAACCAAAGGGTCAGACTGTTGGATCTTTTCGGAAGGGACTTATCATGTTGCCTGATGCAATTTCTGCAAG

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 4
---gtaatatacatgcacataggcttgttttatgattcttccatgaaaatatgttcaatgccctgaatttttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACTTATTATGTTGCCAGAAGCAATTTCTAAAAG
    |||||||  ||| | | |  || |   || |||  |   |||  || |    ||| |    ||||  ||||| |||||| ||||||| ||||| || || || |||||||||||   |||||||||||  |||||||| || |||||||||   ||
gtaataatatatttgctc-tggatttttgccataatttat---tgagtatttcactaattc----aattaatcatgtagGCGTCTGCCAAAACCAAAAGGTCAGACTGTTGGATCTTTCCGGAAGGGACTTACCATGTTGCCTGATGCAATTTCTGCCAG

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtaatat---acatgcacataggcttgttttatgattcttccatgaaaatat--gttcaatgccctgaatttttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACTTATTATGTTGCCAGAAGCAATTTCTAAAAG
    |||| ||   || |     | |  | | | | |  | | | |||  | ||||  ||  ||   |   |  |  |  | ||||||  ||||||| ||| |||| ||||| ||||| ||||| | ||||||||||   ||||||||||||||||| |||  |||
gtgagtaacatcaaacttttctgttgcttgggtcttttgtcccttcatatatatatttgtaaaacaactcaacctgcttcttcagGCGCCTGCCAAAACCACAGGGCCAAACAGTTGGTTCTTTCAGGAAGGGACTTCGAATGTTGCCAGAAGCAATATCTGCAAG

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|351045190|gb|FQ451638.1|FQ451638
EST:     CAAAGCAATCCAGGAGAAAAATAATACTCCCAAGCCTCCGCGAGACCC                         GCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACT
genomic: CAAAGCAATCCAGGAGAAAAATAATACTCCCAAGCCTCTGCGAGACCCgtaatataca ... tttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACT
EST: gi|351054509|gb|FQ451985.1|FQ451985
EST:     CAAAGCAATCCAGGAGAAAAATAATACTCCCAAGCCTCCGCGAGACCC                         GCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACT
genomic: CAAAGCAATCCAGGAGAAAAATAATACTCCCAAGCCTCTGCGAGACCCgtaatataca ... tttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACT
EST: gi|110381438|gb|EC934459.1|EC934459
EST:     TTCAAAGCAATCCAGGAGAAAAATAATACTCCCAAGCCTCTGCGAGACCC                         GCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACT
genomic: TTCAAAGCAATCCAGGAGAAAAATAATACTCCCAAGCCTCTGCGAGACCCgtaatataca ... tttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttatgattcttccatgaaaatatgttcaatgccctgaatttttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACTTATTATGTTGCCAGAAGCAATTTCTAAAAG
                                           tttttcat  CT-rich tract
                     aaaatatgttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatacatgcacataggcttgttttatgattcttccatgaaaatatgttcaatgccctgaatttttcatgcagGCGTTTGCCAAAGCCAAAGGGGCAAACGGTTGGATCTTTTAAGAAGGGACTTATTATGTTGCCAGAAGCAATTTCTAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA