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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttccctttaccttctatgtttaaactttgtgtaagttcatccttaatgaccaaaaggcttcatcatgcag

Basic information

species Vitis vinifera
transcript Vv11s0016g04420.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 16
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttcccttta-ccttctatgtttaaactttg--tgtaagttcatcc-ttaatgaccaaaaggct-tcatcatgcag----------------
  ||| || ||| | || || ||||||||||| || || ||||| ||||| ||||||||||| |||||||||||||| |||||| | || ||  |  ||||| |  || ||  ||||| | |  | ||||| |  |  |  | | |||  ||    | |||| |       | |||| ||                    
ACTGTCCTCTATTCTTTAGCCAGCACACCGGAGCTGGCCTGGGCTGCTGCCAAGCATGGTGGTGTAGTGTACATTCTAGAACTTATGTTACCACTTGAAGgtgataatatttactttagcgtgttttgtttcatatgagattttgagtctatgagctgatgatctgcttattgtcattatttcaaacacttaatgttttt

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G049288_T01 (Zea mays), 5'ss of exon 16
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttccctttaccttctatgtttaaactttgtgtaagttcatccttaatgaccaaaaggcttcatcatgcag---------------------
  ||| || ||| | || || |||||||| || ||||| ||||||||||| ||||||||||| || || ||||||||||||||| | |||||  | ||||||      ||  | |     |  | |   || | || | |    |   |  || || |         ||  |     |                      
GCTGTACTGTATTCTTTAGCCAGCACACCAGAGCTTGCCTGGGCAGCTGCCAAGCATGGTGGTGTTGTTTACATTCTTGAACTTATGTTGCCACTTCAAGgtttgatcttcacttcagtgtattgttactatagttagggctgatattttgtttatcagttgtttttttttttgcataatgtgcatgatactccagtcca

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G001895_T01 (Zea mays), 5'ss of exon 10
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttccctttaccttctatgtttaaactttgtgtaagttcatccttaatgaccaaaaggcttcatcatgcag-----------------------
  ||| || ||| | || || |||||||| || ||||| ||||| ||||| ||||||||||| || || ||||||||||||||| | |||||  | ||||||      ||| | |  || |  | |   || | || | |    |   |  || |   ||    |  ||  ||||   |                       
GCTGTACTATATTCTTTAGCCAGCACACCAGAGCTTGCCTGGGCTGCTGCCAAGCATGGTGGTGTTGTTTACATTCTTGAACTTATGTTGCCACTTCAAGgtttgacctttacttcaacatattgttactatagttagggctgatattttgtttac--ccctgtgtttttgtcataatgtgcataatactgcagtccacatg

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA05G08040.2 (Glycine max), 5'ss of exon 16
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaa---------tatttt--------ccctttacc-----ttctatgtttaaactttg--tgtaagttcatccttaatgaccaaaaggcttcatca--tgcag
||||| || ||||| |||||||||||||| ||||| || ||||| ||||| |||||||| || || || |||||||||||| | |||||||||||| | |||| |          || ||           ||||       |   || |||| | | ||  || |  || || | || |||  || |  | | ||||  |||||
CATGTGCTCTATGCATTGGCAAGCACACCAGAACTGGCCTGGGCTGCTGCCAAGCATGGCGGTGTTGTCTACATTCTTGAATTGCTCTTGCCTTTGAAGGgtagaagacttgtacatcttagttggtcttatttattattattctcatttttagaatctgtttgcagatttatacatattgat-aataatcataatcacgtgcag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA17G12950.1 (Glycine max), 5'ss of exon 17
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaa---------tatttt------ccctttacc--ttctatgtttaaactttgt--gtaagttcatccttaatgaccaaaaggcttcat--catgcag
|||||||| || || |||||||||||||| || || || ||||| ||||| || ||||| || || || |||||||||||| | |||||||||||| | |||| |          || ||       | ||||    |   || |||| | |  ||  | |  || || | || |||  ||||  | | ||  |||||||
CATGTTCTCTACGCATTGGCAAGCACACCAGAGCTAGCCTGGGCTGCTGCCAAACATGGGGGTGTTGTCTACATTCTTGAATTGCTCTTGCCTTTGAAGGgtagaagacttgtacatcttagttggtcatttattattctcatttttagaatcggtttgcagatttatacatattgat-aaaaatcataattccatgcag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S107_71V6.1 (Physcomitrella patens), 5'ss of exon 19
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttcccttt-----accttctatgtttaaa-----ctttgtgtaagt-tcatccttaatgaccaaaaggcttcatcatgcag----------
   ||||| ||| |  ||||||| ||| | |||||||| ||||||||||| ||||||||||| ||||| ||||| ||| | ||| |  | |||  ||||||| | |  |   |   |     |  |  | ||| || |      ||| || |||| | | |   ||  |  || |   |   || ||  |          
AGGGTTCTGTATTCACTGGCAAGTACATCCGAACTTGCTTGGGCAGCTGCCAAGCATGGTGGTGTAGTTTACATACTTCATCTTATTCTACCTGGGCAAGgtcagtgatcatctgatctgaaagttggtctgtctagaacgcattttttgcaagtcttaactaaaaacaagaacaaattaggtcgtgtggatcatgaatt

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: EFJ24089 (Selaginella moellendorffii), 5'ss of exon 17
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttccctttaccttctatgtttaaactttgtgtaagttcatccttaatgaccaaaaggcttcatcatgcag
| |||| | |||||  | ||||| ||  | || ||||| |||||||||||||||||||| || ||||| ||||||||  | ||||| || ||  | ||||||      ||  ||   ||||| || |    || || |  ||| ||||   |  |                        
CGTGTTTTGTATGCTCTTGCAAGTACTTCTGAGCTTGCTTGGGCAGCTGCAAAGCATGGAGGCGTAGTCTACATTCTCCAGCTTCTTTTACCCCTTCAAGgt------ttgtccgggaccttttaag----aatttgggctaaattcacattgcag-----------------------

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: EFJ35138 (Selaginella moellendorffii), 5'ss of exon 17
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttccctttaccttctatgtttaaactttgtgtaagttcatccttaatgaccaaaaggcttcatcatgcag
| |||| | |||||  | ||||| ||  | || ||||| |||||||||||||||||||| || ||||| ||||||||  | ||||| || ||  | ||||||      ||  ||   ||||| || |    || || |  ||| ||||   |  |                        
CGTGTTTTGTATGCTCTTGCAAGTACTTCTGAGCTTGCTTGGGCAGCTGCAAAGCATGGAGGCGTAGTCTACATTCTCCAGCTTCTTTTACCCCTTCAAGgt------ttgtccgggaccttttaag----aatttgggctaacttcacattgcag-----------------------

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|110374849|gb|EC939787.1|EC939787
EST:     AAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAG                         AAGAAATTCCCCTACAGCAGAGAGCAGCAGCTGCCTCATTGCTAGGAAAGC
genomic: AAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattt ... catcatgcagAAGAAATTCCCCTACAGCAGAGAGCAGCAGCTGCCTCATTGCTAGGAAAGC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTTCTTTATGCCTTGGCAAGCACACCGGAACTTGCATGGGCAGCTGCAAAGCATGGTGGAGTAGTGTACATTCTTGAACTTCTCTTGCCTTTGCAAGgtaaatattttccctttaccttctatgtttaaactttgtgtaagttcatccttaatgaccaaaaggcttcatcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG