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

TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag

Basic information

species Arabidopsis thaliana
transcript AT5G05780.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtat--tttctcaggaaactga-----tgcttatactg-tttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag
|||| ||||||||||||||||| || || || |||||||| ||||| ||||| ||||| ||||||||||||  |||||||||||| |||||||||||  | | |||  |  || |     || |    ||| |   ||  ||||      |        | | |||   ||  |||   | |||
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCACGAGTCAATGTTCTCCATGTTCAAGAGGATTAATGgtatgctctatcaaaatcctcaaattttgttgggcctgatccgtgctattgcttcttttgtcctgatgagcacgggctgtttgtggtgcag

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaact---gatgcttatactgtttatgacattgta-gaaatccatgctttt----aacactacctacttgcttttcag
|||| ||||||||||||||||| || || || |||||||| ||||| ||||| |||||||| || ||||||  |||||||||||| ||||| |||||  | |    ||| |   | ||| | |   |  |      |  || | | ||  |  |  |    | ||  | ||  |||   | |||
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 2
-TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattg---tagaaatccatgcttttaac-actacctacttgcttttcag------
 |||||||||| || |||||||| || || ||||||||||||||||| ||||| |||||||| || |||||   |||||| || ||||| ||||||||    |  | ||  |  | ||| |  ||| | |  | ||    |  | |||  || | | |   |  |     ||   |||  |      
GTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCGATGTTTTCCATGTTTAAAAGAATAAATggtatgag-taggaaattttttccttttcttgtatgtctcttttaattgaatatctctgatctaattgaacatgggtttttcttttggtttaca

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgctt---ttaacactacctacttgcttttcag-------
|||||||||| || |||||||| || || ||||||||||||||||| ||||| |||||||| || |||||   |||||| || ||||| |||||||     |  | ||| |  | ||| |  ||| | |    ||  |       |||| |    |||    || |  ||  ||||  |       
TGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgag-taggaaaatttttccttttcttgtatgtc-tgtttcaattgaatatgcctgatctaattgaacattttttttttttggtttacag

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag
|||||||||| || |||||||| |||||||| || || |||||||| ||||||||||| || ||||||||   ||||||||||||||| ||||||||| |     | || |||||    ||   ||||  |  ||   | |     |  | |    | |  | |      ||||||
TGCCCTTTGAAGAAGATGACAAGGACCCAAGTATATGTTTTCTTGACCACAACTACCACGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattattggttgtaagtgatgag-gtatcttttacaatttttatggacaatgttttatgggaatttacaataattgtttcag

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag
|||||||||| || |||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||||||   ||||||||||||||| ||||||||| | |   | || |||||    |   | |||  |  || ||        | ||| |   | |   |  ||   ||||||
TGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttttcgtaaatgatgag-gtctcgcttacaat-ttttatgggcgatttcttatgggaatttatgatt-tgtttcag

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgttta-tgacattgtagaaatccatgcttttaacactacctacttgcttttcag---------------------------------------------------------------------------------------------------------------------
||||||||||||| |||||||| ||  | ||||| |||||  | || |||||||| |||||| | |||||| ||||||||||||||||||| |||||  ||| |  |      | ||   |||| |||    | ||||||   |          ||| | | || |  | ||  | |                                                                                                                     
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtat--tcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgc-agctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag
| || ||||| ||||||||||  ||||||||||| |||||| | ||||||||||| || ||  | |||||  | ||||||||| | || |||||||  ||||        |  || || | || |   || ||||           |||||  |                      
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttct--------tcgtgttttttctttgcttggcattacg----cttgtgcttgcag---------------------

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ23777 (Selaginella moellendorffii), 5'ss of exon 2
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag
| || ||||| ||||||||||  ||||||||||| |||||| | ||||||||||| || ||  | |||||  | ||||||||| | || |||||||  ||||        |  || || | || |   || ||||       |   |||||  |                      
TACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGgtaagttct--------tcgtgttttttctttgcttggcattacg----tttgtgcttgcag---------------------

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|164159164|gb|ES140153.1|ES140153
EST:     TTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: TTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|125149571|gb|EL182665.1|EL182665
EST:     TGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACA
genomic: TGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACA
EST: gi|164132756|gb|ES021857.1|ES021857
EST:     CACAACTATCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAAC
genomic: CACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAAC
EST: gi|124722174|gb|EH813576.1|EH813576
EST:     AGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: AGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|163984651|gb|ES199362.1|ES199362
EST:     CAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: CAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
EST: gi|125124900|gb|EL170608.1|EL170608
EST:     CTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG                         CCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA
genomic: CTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctc ... tgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA