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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctcaaattttatccaacttgtttaattgtgatcatagtgatgcttgttctgcacgttcacattcaaatcatttatgccattaaggccatttttttattaatatattgagccccttggatttgcttttgcttctgcctgcagttatccttttaaatgtaatatgtatcatttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGTCCACCTTGAGTCTTATAGCTCATCCACAGCTGCACTTTTTTTGGGCTAG

Basic information

species Vitis vinifera
transcript Vv18s0041g01360.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 13
gtaagtctcaaattttatccaacttgtttaattgtgatcatagtgatgcttgttctgcacgttcacattcaaatcatttatgccattaaggccatttttttattaatatattgagccccttggatttgcttttgcttctgcctgc--agttatccttttaaatgtaatatgtatcattta-atctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGTCCACCTTGAGTCTTATAGCTCATCCACAGCTGCACTTTTTTTGGGCTAG--------
                                                                                        ||   |    |    |   |  ||||          || |||    ||    |   |  || |||  |    | | |  | |   || |  | || |||||| |||||||| |||||||||||||| ||||||||||| ||||||   ||| ||||||||  | |     |  |     | |||  |||| | || | ||        
--------------------------------------------------------------------------------------cgagatgacaggt--ggtggcagtttgaatttgcatatttcgctacgtctctaacgaacaaagctataataactactctctttttcctcttaaacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTA---GGTTCACCTTGATGCAT-----TTGTGTGTTGTTGCTGTTTTCTGGGTCAAGTTATGCAT

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 16
gtaagtctcaaattttatccaacttgtttaattgtgatcatagtgatgcttgttctgcacgttcacattca-aatcatttatgc-cattaaggccatttttttattaatatattgagccccttggatttgcttttgcttctgcctgcagttatccttttaaatgtaatatgtatcatttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGTCCACCTTGAGTCTTATAGCTCATCCACAGCTGCACTTTTTTTGGGCTAG
                                                                  ||  | |||   |||||   || ||     |   ||| | || || | |   |  ||| ||  | |||  ||  ||  |||  ||  |  ||||||                  ||  |||||||||||||| ||||| |||||||| ||||||||||| ||||||   ||| ||||||||                                        
------------------------------------------------------------------atcaataattccttatgaatataaatattgtcaatttttaaagatttgg---ctgttgaat--gttttatctgatgattgctttttcctctttaaaac----------------attgcagGTTATGGATGTCTTCAATAAAATATCAGAACTCTTCCCTGGAGTA---GGTTCACCTTGA----------------------------------------
















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|30133605|gb|CB918944.1|CB918944
EST:     TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|352769084|gb|FQ471032.1|FQ471032
EST:     TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|110417464|gb|EC983521.1|EC983521
EST:     GTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: GTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|110369051|gb|EC933194.1|EC933194
EST:     TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCTGGAGTATCAGGT
genomic: TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|37183876|gb|CF603230.1|CF603230
EST:     TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTT
genomic: TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTT
EST: gi|46918636|gb|CN547965.1|CN547965
EST:     TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|32268986|gb|CD718145.1|CD718145
EST:     TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|110358161|gb|EC922174.1|EC922174
EST:     ATCAAAATGACAAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: ATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
EST: gi|110421687|gb|EC987987.1|EC987987
EST:     GTATTGCACAGTATCAAAATGACCAGGAG                         GTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT
genomic: GTATTGCAAAGTATCAAAATGACAAGGAGgtaagtctca ... ttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcttctgcctgcagttatccttttaaatgtaatatgtatcatttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGTCCACCTTGAGTCTTATAGCTCATCCACAGCTGCACTTTTTTTGGGCTAG
                                           atttaat  putative branch site (score: 4)
                       ttttaaatgtaatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctcaaattttatccaacttgtttaattgtgatcatagtgatgcttgttctgcacgttcacattcaaatcatttatgccattaaggccatttttttattaatatattgagccccttggatttgcttttgcttctgcctgcagttatccttttaaatgtaatatgtatcatttaatctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGTCCACCTTGAGTCTTATAGCTCATCCACAGCTGCACTTTTTTTGGGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC