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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

Basic information

species Vitis vinifera
transcript Vv03s0038g02760.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
-gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
 |   |  || |  ||  |||   | | ||   |    |||    ||  |          |   |  ||| | |  | |   |   | |  |||| || ||||  ||||||||||||||||| | |||||||||||||| || |||||||| || || ||||||||||||||||| || ||||| ||||||||||| ||||
tgaataatctataagtttttgtagtttatatcttttccttgtttgcatgtagcactgaagtagcggcattgcttaatatgtgtgg-taattctttctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
-----gtcaagcctttctgtgat--tgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
     || ||   |  |  ||||  || | ||| ||||| |   || |  |  |    || |  |||     | ||| ||| |       |  |     || |||||||||||||||||||||||||| | |||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || |||||||| || || ||||
accaggttaaatttaacaatgatattgttttctttagtaccctgttta--ttgagaaattcccatct-----tgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
gtcaagcctttctgtgattgctatctctagtatcagtttgag-atcaacttctttct-----ttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
 ||  ||  |   | |  |||  | | |||| |    || |  | |   ||  || |     | ||||   | ||| ||| || |  |   ||    ||  |||||||||||||||||||||||||| | |||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || ||||| || || || ||||
-tctggcagt---gggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtct-tgtttgattatg-cagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
-----gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
      |      ||  | |   || ||  | || | |    |||  ||||  || || |    | |   |   || ||   || |||| |     | |  |||||| || ||||||||||||||| |||| |||||||| || || ||||||||||| || ||||| ||||||||||| || || || || || ||||||||| 
tttttctttgaatttcttttacatgttacttttattgta---ttggaatcagtttattccaccttttgacttcctcttttcctctctttttg--tttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttat----acagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
         ||   |  ||   || |  | | |  | ||    |  | |||  | |  |||| ||  |  |||| | |  ||   |||   ||| |    |||||| || |||||||| || |||||||| |||||||| || || || |||||||| || ||||| ||||||||||| || || ||||| || ||||||||||
--ttgattattgaatctttttcattttgattgtttgatttgctttga-ttcagtttaactgttgac-tcccattttttttctcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 5
-----gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT-
      |  |  | || | | |||   ||   | |  |  |||||| ||||  ||   | ||       || |||   |   |   | | ||    | |  |||||| || |||||||| || |||||||| |||||||| || || || |||||||| || ||||| ||||||||||| || || || || || |||||||||| 
tgattattgaatcctttt-tcattttgattctttgattttgtttga-atcagtttaactgttgactcccattttttccttaattattgtttt----tgttcacaggTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTT

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 5
-----gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
      |      ||  | |   |||||  | || | |    |||  ||||| || || |    | ||  |   || ||   || |||| |     | |  |||||| || ||||||||||||||| | || |||||||| || || |||||||| || || ||||| ||||||||||| || || || || || ||||||||| 
tttttctttgaatttcttttacatgctacttttactgta---ttggaatcaatttattccaccttttaacttcctcttttcctctctttttg--tttgtccacagGTGTTAAAAACTCCTGTCTCACTAGACATGCTTGGACGCATATTTAATGGCTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
                     | | | |  || ||  ||    | ||  | |   | ||| || ||||       | | ||  | ||    |||  | ||||||||||||||||||| || |||||||||||||| || ||||| |||||||||||||| |||||||| || || || ||||||||||| ||||| ||||
------------------gtttgtttttgctaccaagtt----ttaaagtatcagtgtctata-atatactcacattttccaatgtt---ttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
        | |    || | || ||  || ||  ||||    | |    ||  ||||  | |||   | |||   | |||        ||||    | |  |  ||||  | ||||| || ||||||||||| |||||||| |||||||| |||||||| |||||||||||||| || || ||||| ||  |  |||| || ||| 
ttcctgcccgaattgttttctgttt--taccttaagtaatgttgt----tcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

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|30327898|gb|CD011160.1|CD011160
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACCGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|110730165|gb|EE106929.1|EE106929
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|71862417|gb|DT011472.1|DT011472
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|71861168|gb|DT010223.1|DT010223
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGC
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGC
EST: gi|30325484|gb|CD008746.1|CD008746
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACCGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|32267904|gb|CD717063.1|CD717063
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACCGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|56409259|gb|CX017511.1|CX017511
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|71864966|gb|DT014021.1|DT014021
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|30323990|gb|CD007252.1|CD007252
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACCGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|32248996|gb|CD714815.1|CD714815
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACCGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|71859980|gb|DT009035.1|DT009035
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|110357277|gb|EC920703.1|EC920703
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|32249022|gb|CD714841.1|CD714841
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACCGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|46917753|gb|CN547082.1|CN547082
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|71861589|gb|DT010644.1|DT010644
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|56409525|gb|CX017777.1|CX017777
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
EST: gi|56409500|gb|CX017752.1|CX017752
EST:     GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG                         GTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT
genomic: GAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAGgtataaaatc ... ctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT
                                     ttcttac  putative branch site (score: 2)
                      tttcattgtgtccctt  CT-rich tract
                   atatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

-tcaagcc
- - - - - - - tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctttc