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

CAGCAAAGATGTGATGTTAGATCTGCTTCGGGACCAGTTTCCTGGGGCCAATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttcctttacttttaacaatttcctcttaaatacccatcatcgttcttgttttatgtaactatagccgcccagtcaaccatgtgcattgtattg...

Basic information

species Vitis vinifera
transcript Vv12s0057g01480.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 4
CAGCAAAGATGTGATGTTAGATCTGCTTCGGGACCAGTTTCCTGGGGCCAATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgt---gttccttta--cttttaacaatttcctcttaaatacccatcatcgttcttgttttatgt----aactatagccgcccagtcaaccatgtgcattgtattg
 ||||| ||||| ||| |  | || || || || || |||||||| |||||||||||||||||||| ||||| ||||| |||||   | | |||  ||| |||||    | |  | ||  |||||| |  |||  | |         |     |||    |||| |      || ||||   ||||  |||  ||  ||          
TAGCAAGGATGTAATGCTTCAGCTCCTCCGTGAACAATTTCCTGGAGCCAATGATTTTGGAAGTGAGGTTATTCCAGGTGCAACAAGCATTGGAAAGAGGgtatgcagagattatataaccttttagctctttgttttcttcggtttactgatgtttcctttttgtaataaaaagtata-tagccctttcacacaaatgtc--------

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 4
---------------------------------CAGCAAAGATGTGATGTTAGATCTGCTTCGGGACCAGTTTCCTGGGGCCAATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttcctttacttttaacaatttcctcttaaatacccatcatcgttcttgttttatgtaactatagccgcccagtcaaccatgtgcattgtattg----------------------------------------------------------------
                                  |||||| ||||||||||||| ||||| || ||  |||||||||| || ||||| ||||| |||||||| || || || |                                                                                                     || | |     || | ||                                                                 
GCCTTATATTGCTAGCATGGGTATATATGTTGTTAGCAAAAATGTGATGTTAGACCTGCTCCGTGAGAAGTTTCCTGGTGCAAATGACTTTGGGAGTGAAgtgattcctggtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactttcttgttattttcctgcatggtaaattagcatgcaattttttgagaatatgtacggcatgtttgtgtgtattcacag

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 4
CAGCAAAGATGTGATGTTAGATCTGCTTCGGGACCAGTTTCCTGGGGCCAATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttcctttacttttaacaatttcctcttaaatacccatcatcgttcttgttttatgtaactatagccgcccagtcaaccat--gtgcattgtattg---------------------
 |||||| | ||||||||||| ||||| || ||  |||||||||| || ||||| ||||| |||||||| || || || || |||||  | ||| |||| |||||||||||||      |    ||||  | |||   |  | |  | ||  || | ||   || | | |     |  |  |    |  |    |||||| |                     
TAGCAAAAACGTGATGTTAGACCTGCTCCGTGAGAAGTTTCCTGGTGCAAATGACTTTGGGAGTGAAGTGATTCCTGGTGCTACTTCTATTGGAATGAGGgtatgtgttccttc-----tggttatttaatattacgaaaactttcttgtcattttcttgcatagcaaaatttagcatgcaattttttagaatgttgtatggcatgtttgtgtatattcacag

upper sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 5'ss of exon 3
CAGCAAAGATGTGATGTTAGATCTGCTTCGGGACCAGTTTCCTGGGGCCAATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttcctttactt-ttaacaatttcct-cttaaatacccatcatcgttcttgt-tttatgtaactatagcc-gcccagtcaaccatgtgcattgtattg-------------------------------------------------------
 |||| |||||| ||| ||||  | || ||| | ||||||||||| || ||||| |||||||||||||| || || || || |||||||| ||| |||| ||  |||||  | | | | || ||||  ||    ||  || |  ||  ||   |  || | | |    |||| |   ||      |  ||   || |  | | |                                                       
AAGCAGAGATGTAATGCTAGACTTACTACGGAATCAGTTTCCTGGAGCTAATGACTTTGGAAGTGAAGTCATTCCCGGTGCCACTTCCCTTGGACTGAGGgtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcag

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|33409675|gb|CF215302.1|CF215302
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|110688952|gb|EE068088.1|EE068088
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|161718175|gb|FC065663.1|FC065663
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|110689182|gb|EE065182.1|EE065182
EST:     ATGATTTTGGAAGTGAAGTTATACCANGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|30325486|gb|CD008748.1|CD008748
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|352776770|gb|FQ472657.1|FQ472657
EST:     AACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
genomic: AACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|30324817|gb|CD008079.1|CD008079
EST:     ATGATTTTGGAAGTGAAGTTATACCANGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|71863688|gb|DT012743.1|DT012743
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|30324290|gb|CD007552.1|CD007552
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|33403137|gb|CF208764.1|CF208764
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|30253354|gb|CB970905.1|CB970905
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTGGGAGGACATTGGTACAATTGAG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAG
EST: gi|110703129|gb|EE079706.1|EE079706
EST:     ATGATTTTGGAAGTGAAGTTATACCANGGGCAACTTCCCTCGGATTGAGA                         GTGNCA-GCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGA
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTG-CAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGA
EST: gi|27579307|gb|CB002002.1|CB002002
EST:     ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGA                         GTGCAAGCTTACTTGTATGATGGCTACTG
genomic: ATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttc ... atctctgtagGTGCAAGCTTACTTGTATGATGGCTACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCAAAGATGTGATGTTAGATCTGCTTCGGGACCAGTTTCCTGGGGCCAATGATTTTGGAAGTGAAGTTATACCAGGGGCAACTTCCCTCGGATTGAGAgtatgtgttcctttacttttaacaatttcctcttaaatacccatcatcgttcttgttttatgtaactatagccgcccagtcaaccatgtgcattgtattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG