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

...atgttgcatcagtattgacaccctgacaagtttttttccccttgttcttgaacacgttattatggttatcctgagattacttgtcgattcatatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTCTTTTCAAGATTCTGCACACCAATATTCTTGGAG

Basic information

species Vitis vinifera
transcript Vv04s0023g00380.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 6
atgttgcatcagtattgacaccctgacaagtttttttccccttgttcttgaacacgtt----attatggttatcctgagattacttgtcgattcatatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTCTTTTCAAGATTCTGCACACCAATATTCTTGGAG
   ||  ||    ||| |     |  ||| ||||||     || || ||  ||  | |    |||  |   || || |||  | |  |  ||     |   ||||||||||| ||||| ||   |||||||||||||||     | || |||||||||||||||||||| ||||||||||| ||||||
ggattctatactcattaattggtt--caatttttttatatattctttttttacctggttcagatttggtacatgctaaga--attgattaatcttgttaactagGTTGAAGAAAAACTGGATGGTGGACAAGGGAAAACTTCAGTTCGGCGCTTCTTTTCAAGATTCTGTACACCAATATTTTTGGAG

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G38640.1 (Glycine max), 3'ss of exon 6
atgttgcatcagtattgacaccctgacaagtttttttccccttgttcttgaa-cacgtt-----attatggt-tatcctgagattacttgtcgattcatatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTCTTTTCAAGATTCTGCACACCAATATTCTTGGAG
     |||    |  | | ||  | |    ||   ||     | ||    ||  |  ||     | | ||||  || || |||  | || |  ||     |   ||||||||||| ||||| ||   |||||||||||||||     |  | ||||||||||||||||| || ||||||||||| ||||||
----ggcacggattct-atactttaattgattcaattttttatattaaaaaaatatcttggtcaaatttggtacatgctaaga--atttattaatcttgttaactagGTTGAAGAAAAACTGGATGGTGGACAAGGGAAAACTTCAGTTAGGCGCTTCTTTTCAAGATTTTGTACACCAATATTTTTGGAG
















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|110375514|gb|EC940507.1|EC940507
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|33405511|gb|CF211138.1|CF211138
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|30303671|gb|CB980465.1|CB980465
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|71867156|gb|DT016211.1|DT016211
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAA-TGGAGGAA                         GT-GAAGAGAAACT-GAGTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTC
EST: gi|110386306|gb|EC950891.1|EC950891
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|34320010|gb|CF372764.1|CF372764
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110403098|gb|EC964255.1|EC964255
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110398724|gb|EC965198.1|EC965198
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110393823|gb|EC959339.1|EC959339
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110689638|gb|EE066037.1|EE066037
EST:     CAGATTCAAAGGCATCCCCGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: CAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|30303609|gb|CB980403.1|CB980403
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110369298|gb|EC933452.1|EC933452
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|161719466|gb|FC066414.1|FC066414
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110685575|gb|EE062425.1|EE062425
EST:     TTGCTTGGAGATCAGATTCTAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         ATTGAAAAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110418308|gb|EC984450.1|EC984450
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|71866927|gb|DT015982.1|DT015982
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
EST: gi|110418385|gb|EC984534.1|EC984534
EST:     TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA                         GTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC
genomic: TTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAAgtatgttttt ... atatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaacacgttattatggttatcctgagattacttgtcgattcatatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTCTTTTCAAGATTCTGCACACCAATATTCTTGGAG
                                             atatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttgcatcagtattgacaccctgacaagtttttttccccttgttcttgaacacgttattatggttatcctgagattacttgtcgattcatatgtttagGTTGAAGAGAAACTTGAGTCTGGACAAGGGAAAACAAGTTTCCGCCGCTTCTTTTCAAGATTCTGCACACCAATATTCTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - tgcatca
- - - - - - - - - - ccctgac