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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctaaataccctacgtctcttcattttcttctaacgttaaccatcgtacattacagcaatttcctaatcatttttatccttcgtattgctcttttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGACGATTTTATAGCAGATGCCTTAAGGGGTACTGGATTTTACCAAAAGGCTC

Basic information

species Vitis vinifera
transcript Vv14s0030g01610.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
gtctaaataccctacgtctcttcattttcttctaacgttaaccatcgtacattacagcaatttcctaatcatttttatccttcgtattgctcttttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGACGATTTTATAGCAGATGCCTTAAGGGGTACTGGATTTTACCAAAAGGCTC
             | |||    ||  | || || ||   | ||||| |   |   | || ||   | ||||   | |    || | |  ||  ||     ||||| ||||| ||||| |||||||| |||||||||||||| || || || || || || ||||| ||||| || || || || ||  ||||||| ||  || 
--------gtaagatgtcgaaacaagt-ctactcacaa-acccatctt---tctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
















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|110392295|gb|EC957614.1|EC957614
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|110708135|gb|EE085328.1|EE085328
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|110363177|gb|EC926749.1|EC926749
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|110695405|gb|EE073382.1|EE073382
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|34361753|gb|CF403338.1|CF403338
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|110384122|gb|EC948538.1|EC948538
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|110401148|gb|EC967744.1|EC967744
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|26261545|gb|CA812608.1|CA812608
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTGTACGTCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
EST: gi|26262618|gb|CA813681.1|CA813681
EST:     GTGAGCCTTGCCCAATGTGCTTTGGTGCTGTACGTCTTTCAAGAATTAAG                         AGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC
genomic: GTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaatac ... tttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattacagcaatttcctaatcatttttatccttcgtattgctcttttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGACGATTTTATAGCAGATGCCTTAAGGGGTACTGGATTTTACCAAAAGGCTC
              tcctaat  putative branch site (score: 2)
                                      ttgctctttt  putative PPT
                 taatcatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaaataccctacgtctcttcattttcttctaacgttaaccatcgtacattacagcaatttcctaatcatttttatccttcgtattgctcttttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGACGATTTTATAGCAGATGCCTTAAGGGGTACTGGATTTTACCAAAAGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG