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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcattgattactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatactttaaatgatattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC

Basic information

species Vitis vinifera
transcript Vv08s0105g00390.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 4
gttggttcattgattactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatactttaaatgatattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
    |||       | |||  ||  ||| |   |  || || | |        |  || ||  |   |    || ||||  ||||    |||||||||| |||||||| ||  | ||||| ||||| ||||| || ||   |||||||  ||||||||| |||||||||||||| |||||    |||||| 
----gtttgaatccttctctaattgattatctttt-tctaagtctaacaaacatatatattttactgaaccgaactgat--tcttgaccagGTTATTGCTGATCACTTATCAGCCGAAGAGGTTGAGGACATAAAGGACATGTTCAAGGTGATGGATACAGATAATGATGGTATAGTCTCTTATGAAGAGT

upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 4
---------gttggttcattg----attactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatacttta----aatgata------ttcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
          ||  || ||      | |  ||   ||  ||||    || ||  ||   | |     ||||  |  | | | |||     | ||| |      |||||   ||||||||||| |||||||||||  ||||||| ||||| ||||| || ||   |||||||  ||||||||||||||||||||| || || ||    |||||| 
gttcgaaacctttctttatcacggaactgatctagtgtgttttagtgcaccctttt---tctagataccatcatggagacagtttgctttactgacaaagtggttcttgactagGTTATTGCTGATCACTTGTCAGCTGAAGAGGTTGAGGACATAAAGGATATGTTCAAGGTGATGGATACTGATAATGATGGCATAGTTTCTTATGAAGAGT

upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G088361_T01 (Zea mays), 3'ss of exon 4
-------------------------gttggttcattgattactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatactttaaatgatattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
                           || |  | ||  | ||   ||||||  |   ||   | |  |||    |  | || ||||   | |    || || ||  |||   ||||||||||| |||||||||||  ||||||| ||| | ||||| || ||   |||||||  |||||||||||||||||||||||| || ||    |||||| 
gttcgaaatctttctttatagtgaaactgatctaatg--tgctttaatgcatcctgtttctagctaccatggaaacgattcactttactgaca----aactggta--cttgactagGTTATTGCTGATCACTTGTCGGCTGAAGAGGTTCAGGACATAAAGGAGATGTTCAAGGTGATGGATACTGATAATGATGGTATAGTTTCTTATGAAGAGT

upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 4
--------gttggttcattgattactcctatgc-------atttttaatcatccaattatgtttgctct-ccattttaaaaat-act-------ttaaatg-atattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
         ||| |  ||||| |  |   || |        | ||| ||  |||  |||| | |||  |  || || |  | | |||       |||  || || |  ||   ||||| ||||| ||||| |||||| |||| |||||||| || || || ||   ||||||||  ||||||||||| |||||||| ||||| ||    ||||| |
gtctgtatcttgctctattgaattttttcatcctggtctggtattttattctccc-ttatctctgccatatcaattcaggattgactgataagattaggtgtatgtgtttgactagGTCATTGCTGATCATTTGTCTGCTGAGGAAGTTGAGGATATAAAGGATATGTTCAAGACTATGGATACTGACAATGATGGAATTGTATCTTATGAAGAAC

upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 6
gttggttcattgattactcctatgcatttttaat--catccaattatgtttgctctccattttaaaaatactttaaatg-atattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC-
             ||| | |  ||||| | |  |   |||  |     |||  | | || | |   |   ||   | |  | |||  ||   |||| ||||| |||  ||| || | ||||||||||||||||||||||||   ||||||||||||||||| |||||||||||| ||||| || || ||||| | 
-------------ttagttcactgcatctctggtaatatcttaagccatttcttttacagtatgtcagagctaagattttacatttgtaaacaggTCATTGCTGATTTCTTATCCAATGAAGAAGTTGAAGACATCAAAGATATGTTCAAGAAGATGGATAATGATAATGATGGCATTGTTTCCATTGAAGAACT

upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 4
gttggttcattgattactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatactttaaatgatattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
||| ||||| ||  | |||   ||   | |||| |     |||   ||| |  |  || | | |  ||   |   | |||||  |||  |||| ||||| |||  ||| || | ||||||||||||||||||||||||   ||||||||||||||||| |||||||||||| ||||| || || ||||| |
gttagttcactgcat-ctctggtgatatcttaagcc----attgcttttacagt--atgtcagagctaagatt--ttatatttgtatacagGTCATTGCTGATTTCTTATCCAATGAAGAAGTTGAAGACATCAAAGATATGTTCAAGAAGATGGATAATGATAATGATGGCATTGTTTCCATTGAAGAAC

upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggttcat-tgattactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatactttaaatgatattctt--atgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
||| ||| || |||| |   ||   |||| ||||| |      |  ||   ||    |     || |||  || | | || || ||  |   |||||||||||||    || ||||| |||||||| ||||||||||||| |  |||||| |||||||||||||||||||||||||| || || || || ||| 
gtttgtttatctgataaactct---cattcttaattacttgcatgagtc-acttcttaaacggaagatatctttactaatcttattcaaaccagGTTATTGCCGAATTTTTATCTACGGAAGAAGTAGAAGACATCAAAGTAATGTTCAACAAGATGGATACTGATAATGATGGTATAGTTTCCATTGAGGAGT

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|110702917|gb|EE079305.1|EE079305
EST:     GGCTTAAGCAGTTTTCAATGATGAACAGATTCAAAAGAAAGGCCCTGAGG                         GTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCG
genomic: GGCTTAAGCAGTTTTCAATGATGAACAGATTCAAAAGAAAGGCCCTGAGGgttggttcat ... tcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCG
EST: gi|33405399|gb|CF211026.1|CF211026
EST:     GGCTTAAGCAGTTTTCAATGATGAACAGATTCAAAAGAAAGGCCCTGAGG                         GTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCG
genomic: GGCTTAAGCAGTTTTCAATGATGAACAGATTCAAAAGAAAGGCCCTGAGGgttggttcat ... tcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaattatgtttgctctccattttaaaaatactttaaatgatattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC
                                          tattctt  CT-rich tract
                    attttaaaaatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcattgattactcctatgcatttttaatcatccaattatgtttgctctccattttaaaaatactttaaatgatattcttatgtagGTTATTGCCGATCACTTGTCTACTGAAGAAGTTGAAGACATCAAAGAATCGTTCAAGAAGATGGATACTGATAATGATGGTATTGTCTCGATAGAAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA