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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttcactatgcatttcaatgtgatctttgattgctgcactattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT

Basic information

species Vitis vinifera
transcript Vv10s0003g03950.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 6
aattttcactatgcatttcaatgtgatctttgattgctgcac-tattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
           ||  | |  |||| ||   || || | |  | || |||  ||| ||      |      ||| |||   ||     |||| |  |   |||||| | ||||| |||||||| ||||||||||||||| | ||||||||||| || |||| |||||| || ||||||||||| || ||||||||| |||||
----------gtgtgtgttcatgttattcatgttttcagttcataatatgcacttgtctgattcaa----aatcatatccttggaa-tgttattttcacagTGCAATTATGGATTGTGTTGGATGTGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGAT

upper sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
aattttcactatgcatttcaatgtgatctttgattgctgcactattat-tgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
    ||    |   |||||  |||| |||    ||        ||||  ||  |  |  |   ||       | |  ||  ||    | | || |||  |||||| | |||||||||||||| || |||||||| ||||| ||||||||||| || ||||||||||||||||||||| ||||||| ||||||||| |||||
---gtttgtgacatatttcc-tgtgttctcaacttctcatttcattagatgcattatgaaccacttgaatccttacccatgtaacattttatttatt--agTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT

upper sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 7
aattttcactatgcatttcaatgtgatctttgattgctgcactattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
    ||    |   |||||  ||   |  ||  ||  |    ||    |||     |  |  |  | || |||  ||| ||       | || |||  |||||| | |||||||||||||| || |||||||| ||||| ||||||||||| || |||| ||| |||||||||||  ||||||| ||||||||  |||||
---gtttgtgacatatttc--tggtgttcttatttcataagatacatatgaaccacttgtatccttacccatgtaacattt-------tcttgatt--agTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCTTGGCCTTGGAACTGCTCTGAAAATTCTTTTCTCCGTTGAT

upper sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G23150.2 (Glycine max), 3'ss of exon 7
aattttcactatgcatt-tcaatgtgatctttgattgctgcactattattgac---tggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
 | |     ||    || || || |  | ||  | | |||    |   |  ||   || || ||  |  || |||||  |   ||||||   | |  | || |||||||||||||| ||||| || |||||||| |||||| | ||||| ||||||||||||| |||||||||||||||||| || || || |||||| |||||
cactccttttacttgttctccatttattattctactactgattcaacttacacttttgatttatctcattggcaatggaatg-ttattt---tgtggaatgcagTGCATTGATGGATTGTGTAGGATGTGAGAAATGTCGATTATGGGGTAAGCTTCAGGTTCTTGGTCTTGGAACTGCATTAAAGATTCTCTTCTCTGTTGAT

upper sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 7
------aattttcactatgcatttcaatgtgatctttgattgctgcactattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
        | | || |    |||  | |      |    || |  ||||  |  |   || || ||  |  || |||||  |    ||| | | |||  | || |||||| ||||||| ||||| || |||||||| |||||| | ||||| || |||||||||| |||||| ||||||||||| || || || |||||| |||||
ttacttgctctccatttattattctactactgattcaacttac-acactgctgctt-ttgatttatctcattgacaatggaa----tatatttttttggaatgcagTGCAATGATGGATTGTGTAGGATGTGAGAAATGTCGATTATGGGGCAAACTTCAGGTTCTTGGTCTCGGAACTGCATTAAAGATTCTCTTCTCTGTTGAT

upper sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
aattttcactatgcatttcaatgtgatctttgattgctgc----actattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
    |||   |  | ||| | |    |  ||||    ||     | |   | ||||| | | |      | |   |     | ||   ||   || ||||| |||||| | ||||||||||| ||||||||||| || || || ||||||||||||||| |||  ||||| || |||||||||||||| || ||| || |  ||
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT

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|110728702|gb|EE104502.1|EE104502
EST:     AATGGACCTGAATTGAAGCAGCAAATACAAAAACAGTTCAAAAACATTAN                         TGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCNACTTTGGGGAAAGCT
genomic: AATGGACCTGAATTGAAGCAGCAGATACAAAAACAGTTCAGAAACATTAGgtctttctca ... ttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCT
EST: gi|110420546|gb|EC986821.1|EC986821
EST:     CCTGAATTGAAGCAGCAGATACAAAAACAGTTCAGAAACATTAG                         TGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCT
genomic: CCTGAATTGAAGCAGCAGATACAAAAACAGTTCAGAAACATTAGgtctttctca ... ttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCT
EST: gi|110722811|gb|EE099409.1|EE099409
EST:     AATGGACCTGAATTGAAGCAGCAAATACAAAAACAGTTCAGAAACATTAG                         TGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCT
genomic: AATGGACCTGAATTGAAGCAGCAGATACAAAAACAGTTCAGAAACATTAGgtctttctca ... ttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT
 tattgac  putative branch site (score: 2)
                                  ttatttctgttttc  putative PPT
                        aatgatacaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattttcactatgcatttcaatgtgatctttgattgctgcactattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT

- - - - ctatgca
- - - - - - - - - caatgtg
- - - - - - - - - - - - - - - - - -gctgcac
- - - - - - - - - - - - - - - - - - - - - - - - tgactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatacaa