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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgattgcacttgtccttacatatcttttccaatgttgattcttctttgaactcaattgtgtacattgttttaccctttacctttcccttacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACATAAGTTTACACCAAGATGGTTTGATTTTACTGAGGAAGTCACACCTACA

Basic information

species Vitis vinifera
transcript Vv06s0004g04930.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 9
gttgattgcacttgtccttacatatcttttccaatgttgattcttctttgaactcaattgtgtacattgttttac----cctttacctttccctta---cttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACATAAGTTTACACCAAGATGGTTTGATTTTACTGAGGAAGTCACACCTACA
        | ||      || | ||    |  | | |  |   |  |  ||       ||| ||  ||||||  |      |||| ||||   ||    | |||||||||||||||||||||  | || |||||||||| ||||||||  || || ||||  || |||||||||||||||||||| ||||| ||||| ||||| || 
------ccctctctcaaatagaaatgggcttaagtttcaacaatcatcagagagatgctgt-taggttgtttcccagggtatttatctttgttttgtttcctttcagTTTGGAGGAGAGGCAGCGTGCTGAAAAGAGAAGCCGAGAGGAGAAAGGGCATAGCTTCACACCAAGATGGTTTGATTTAACTGAAGAAGTGACACCAACT

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 9
------gttgattgcacttgtccttacatatcttttccaatgttgattcttctttgaactcaattgtgtacattgttttaccctttacctttcccttacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACATAAGTTTACACCAAGATGGTTTGATTTTACTGAGGAAGTCACACCTACA
       |  | |  |  ||  |||   | ||      |||        | || |||  |   ||     ||  || ||   ||||   ||    |    ||||||||||||||| |||||  | || |||||||||| ||||||||  || || ||||  || |||||||||||||||||||| ||||| ||||| ||| | || 
acccctctcaaatagaaatgggcttgagtttcaccaataatcagagagatgctgtgaggttgtttcc---cagggtatttatctttggtttgttttc---tttcagTTTGGAGGAAAGGCAGCGTGCTGAAAAGAGAAGCCGAGAGGAGAAAGGGCATAGCTTCACACCAAGATGGTTTGATTTAACTGAAGAAGTGACATCAACT

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 9
---gttgattgcacttgtccttacatatcttttccaatgttgattcttctttgaactcaattgtgtacattgttttaccctttacctttcccttacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACATAAGTTTACACCAAGATGGTTTGATTTTACTGAGGAAGTCACACCTACA
        || || |  |   |||| |   ||| | || |||  |  |   |   |  |    |  || |     ||   | |   | |  ||| | |  |||||||||||| | |||| |  | ||||||| || |||||| ||||| |  ||||| |||||||| |||||||||||||| ||||| ||||| ||| | || 
ttctacagttacaatatttagtaca-acaatttgctattttgccttctgagttttcctaggcata-acttcacactaagatgt-tgtgtgtctttcctaacagTTTGGAGGACAAGCAACGCACTGAAAAGAAAATCCGAGAAGCCAAAGAGCATAAATTTACACCGAGATGGTTTGATTTAACTGAAGAAGTGACATCAACT

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|22008495|gb|BQ793529.1|BQ793529
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAACCCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|22012903|gb|BQ797937.1|BQ797937
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|33405066|gb|CF210693.1|CF210693
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|110716660|gb|EE091846.1|EE091846
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|33405148|gb|CF210775.1|CF210775
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|110688435|gb|EE066987.1|EE066987
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|110378376|gb|EC943506.1|EC943506
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|110705363|gb|EE082145.1|EE082145
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
EST: gi|30252533|gb|CB970084.1|CB970084
EST:     TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAG                         TTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA
genomic: TATGCACTTGAAAAGGGAGATCTATCAAAAGCTGGTGCTGAAAAGAGCAGgtctctctca ... tacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgaactcaattgtgtacattgttttaccctttacctttcccttacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACATAAGTTTACACCAAGATGGTTTGATTTTACTGAGGAAGTCACACCTACA
                                         cccttac  putative branch site (score: 3)
                   cattgttttacccttt  CT-rich tract
                    attgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgattgcacttgtccttacatatcttttccaatgttgattcttctttgaactcaattgtgtacattgttttaccctttacctttcccttacttttcagTTTGGAGGAGAGGCAAAGAGCAGAAAAGAGAAACCGAGAGGCCAAGGGACATAAGTTTACACCAAGATGGTTTGATTTTACTGAGGAAGTCACACCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - -gcacttg
- - - - - - - -ccttaca
- - - - - - - - - - - - - - - ccaatgt
- - - - - - - - - - - - - - - - - - - - - - - - -gaactca