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

gtgagtctgaatttgagccctttttgcttcgttttaggctctgatcttgaactgagaaatgttaatttagggttttggttttctttttcttttttttggttgaattttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG

Basic information

species Vitis vinifera
transcript Vv12s0059g01400.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G43550.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtgagtctgaatttgagccctttttgcttcgttttaggctctgatct-tgaactgag----aaatgttaatttagggttt------tggttttc----tttttcttttttttggttgaattttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG
                                    |     |   ||||    |||  || | | ||| ||   |  ||   |||| || |    || | | ||| |     ||       | | ||     || || |||| |||| |||  | ||  | |||||| || || || ||| ||||||||||||| ||||  |||||||||||||| |||||||| ||||||||||||||||| ||||| ||  |||||
gtctgtcctcacatctcaatcacccttttcttatcttcttcttcgttttgttaacttgatgatgcttttgagtacccaattgatgaattgtgagtaaagtctcaatcttttccttgttgcacgctgttgctgattgtttttttgtttgattgggtgtttttatagATATCTGTGTCCTGAGCCGTATCCGGAGGCCAATATGGAGTTCCTCAAGTCAAATGGGATCAAGCTTTTTCAGTTTGGGATTGAGGGTCATAAG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 1
gtgagtctgaatttgagccctttttgcttcgttttaggctctgatcttgaactgagaaatgttaatttagggttttggttttctttttcttttttttggttgaattttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG
             |||  | ||||   | |    | |      ||| |||    ||   |  |  |||        | | ||  |  |  |||  |||| ||  ||||  | |||||| || || || ||| ||||||||||||| || |  |||||||||||||| |||||||| ||||||||||||||||| ||||| ||  |||||
------------atgatgctttttgagtacccaattgatg--aatcgtgagtaaagtcttcatcttttcctcgcacgctgttgctgattatttgattggatgttttttt-tatagATATCTGTGTCCTGAGCCGTATCCGGAGGCCAACATGGAGTTCCTCAAGTCAAATGGGATCAAGCTTTTTCAGTTTGGGATTGAGGGCCATAAG

upper sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G32960.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------gtgagtctgaatttgagccctttttgctt--cgttttaggctctgatcttgaactgagaaatgttaatttagggttttggttttctttttcttttttttggttgaattttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG------
                      ||| ||| |  |||    | ||   |||   | |||||| | |  | |     |      | ||  ||  |   |   |||||  |  | | ||| |   | | |  |   |  ||||   | || || ||| | ||||| |||   || |   |||||||||| || ||||| ||||  |||||||||||||| |||||||| | ||||      
gtataaagctactatgatcaattgactcttatattggaaacgttggacttgttgatttaggtttttgtgtgtgttttt----ttttccttctgacatcaagtttttgtggtttgtttgtgtatgggaaatgtgtgaagATCTTTGTGTCCAGAGCCATATCCTGAGAACAACATGCAGTTCCTCAAATCCAATGGAATTAGTCTTTTTCAGTTTGGCATTGAAGGCTCTAAGTCCAAG

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|30256135|gb|CB971978.1|CB971978
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|351015527|gb|FQ447356.1|FQ447356
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGTTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|26258262|gb|CA809325.1|CA809325
EST:     CTAGGTCTCCGTTCAATCAT                         ATTCCTTTGCCCGGAGAGGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: CTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|26257485|gb|CA808548.1|CA808548
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|351045015|gb|FQ449269.1|FQ449269
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGTTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|71857429|gb|DT006484.1|DT006484
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|110379464|gb|EC944660.1|EC944660
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|351022573|gb|FQ447095.1|FQ447095
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGTTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|351034099|gb|FQ448017.1|FQ448017
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|110362858|gb|EC926416.1|EC926416
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|29785487|gb|CB342539.2|CB342539
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|30253078|gb|CB970629.1|CB970629
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
EST: gi|30256204|gb|CB972047.1|CB972047
EST:     GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCAT                         ATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC
genomic: GACACAGCCAACTTCGCCTTCTTGCAAACCCTAGGTCTCCGTTCAATCATgtgagtctga ... tttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatttagggttttggttttctttttcttttttttggttgaattttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG
 tgttaat  putative branch site (score: 3)
                                            ttttcattt  putative PPT
                  ttttctttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctgaatttgagccctttttgcttcgttttaggctctgatcttgaactgagaaatgttaatttagggttttggttttctttttcttttttttggttgaattttcatttagATACCTTTGCCCGGAGACGTATCCGGAGGCGAATAATGAGTTCCTCAAGTCGAATGGGATTAAGCTTTTTCAGTTTGGAATTGAAGGATATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG