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

GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag

Basic information

species Vitis vinifera
transcript Vv11s0037g00110.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 5
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag
|| |||||||||||||||||||| || || || || |||||||||||||| ||||| || ||||| || |||||  |||      |  |   |  | |  |||||   ||    |   ||   || | ||  ||| |  |||     |                                  
GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCGgtttg---tcaaacttcatattgtatttcttttggtacaagtaggccttgatactattcttgtttg-aacag---------------------------------

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 6
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag
|| |||||||||||||| || || || || ||||| |||||||||||||||||||| || ||||| || |||||  |||     ||      |||| ||||   || |  |   || ||    |   | | |  |  |||| ||  |  |||    |  | |                    
GTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCGgt-----ttgtgaacttgtgtacttcataaagcacttctttt----ccttccaagtctaaatttgatattctttctatttggacag-------------------

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 6
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcc-cagtcaatacgcctattcttggtttgcag-
 ||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| || |||||||| || || | ||||   |||||     ||||      |||||| |    |  |||| ||   |  | || ||||| || | |||    ||| |        ||   || |||  || 
-TAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAGtaa---tttca-----gtct-----ctacattttattcg--acaattacacat-actggattttttgttcattaagtagtgagcttatggatctctgctttataga

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag
|| ||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| || |||||||| || || | ||||   || || | | | |    ||||  |||| | |  |||||  || ||||  || |  || ||   ||||   ||| |        ||   || |||  ||
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaa---ttccagtctcgac----attt-tatta-gacaattacacata-ctagattttttgttcat--caattaatagtgaggttatggatctctgctttatag

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 5'ss of exon 5
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag
|| ||||| |||||||| ||||| || || || |||||||| |||||||||||||| || ||||| || ||||| ||||  | | | |   |     | | ||  ||| |    |||  | ||     |    ||  |  | | |  || |   |   |||  |   | | | |        
GTTGCTGATTCACTTGAAAAAGGAACAGAACATGAAGATGAGTACATGATCAGTGAAAAGGAGCTTCTTGTTAACAGgtttatactgctccagctctttccataaacact----ctgagataatgtaattttttta-aggtcaagaaaactgataacaaatgtgaa-agtgtag--------

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S303_47V6.1 (Physcomitrella patens), 5'ss of exon 5
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag
|| || || ||  | || || || || || || |||||||| ||||||||||||||||| ||||| || ||||| |||||    ||||  | ||  |    ||   |         | |      |  |        | ||| |  |   |   ||  ||       | |   | |||    
GTGGCAGATTCTTTAGAAAAGGGCACGGAACATGAAGATGAGTACATGATCAGTGAGAAGGAGCTTCTTGTTAACAGgtatgtctttccctttttcccttgataggctgggatgtcgatgtttagaattgatgcctcaatttgttttgcgtta-aggaaacgaagtgaatgcagattt----

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|110415074|gb|EC980946.1|EC980946
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|34543363|gb|CF511595.1|CF511595
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGACCATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|34543277|gb|CF511509.1|CF511509
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|349827547|gb|FQ422415.1|FQ422415
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|351018852|gb|FQ425754.1|FQ425754
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|33408903|gb|CF214530.1|CF214530
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|110406906|gb|EC972493.1|EC972493
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|351041121|gb|FQ444098.1|FQ444098
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|33408990|gb|CF214617.1|CF214617
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|349827476|gb|FQ422344.1|FQ422344
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
EST: gi|110362846|gb|EC926403.1|EC926403
EST:     GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG                         ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT
genomic: GAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagattt ... tggtttgcagATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag

- - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT