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

GTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATTgtactctcatactctctttttcttctacttttattggttttacacatgtgtgaaactaacaaatctcatcttgtgtgtttgaag

Basic information

species Arabidopsis thaliana
transcript AT1G63830.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G63830.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 5'ss of exon 5
GTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATTgtactctcatactctctttttcttctacttttattggttttacacatgtgtgaaactaacaaatctcatcttgtgtgtttgaag-----------------------------
|| || || ||||| || || || || || || ||||||||  | || || |||||||||||||| ||||||||  ||||||| || ||||| |||||||| |||   ||   || |  | |  ||||| |   |||    | || | |  |  |    || | |  | || |  |  |                              
GTGTTTCTGTGCTTTGGTAATTCAGTTGCTTCAACCCGCTTCTTGCTCCAAGATGAATTCAACATACAGACAACTAAATGCGATAACTGCATCATTgtactgtcactgtcctcttgttgtttg-ttttactaacttt---taggtataattcctatgt-tccctttctatgagactataacactgcagaagatcactcttttcctgtag

upper sequence: AT1G63830.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G065696_T01 (Zea mays), 5'ss of exon 6
GTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATTgtactctcatactctctttttcttctacttttattggttttacacatgtgtgaaactaacaaatc---tcatcttgtgtgtttgaag-------------------------
|| |||   |||||||| ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||||| ||||| || || |       |   |     |     | |  ||  || |     |||  |  | || |     |   ||| ||     |  ||| |                         
GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCgtgcgtagtcgcggccggccacgcgcgcctcgatccgtctcctg-atgacttgatctgatcttccgaatcagctgactcgactgacgctactcatcttcctcgtcgttgcag
















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|125277681|gb|EL291766.1|EL291766
EST:     TGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAGCCAAGTTGCTTGCA
genomic: TGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATTgtactctcat ... gtgtttgaagGGATTTATGTTCTGCCTCAGCCAAGTTGCTTGCA
EST: gi|124851167|gb|EH935604.1|EH935604
EST:     TTCAACATCCAGACAACACAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAGCCAAGTTGCTTGCATATTCTCTATAGTTG
genomic: TTCAACATCCAGACAACACAATGCGACAATTGCATAATTgtactctcat ... gtgtttgaagGGATTTATGTTCTGCCTCAGCCAAGTTGCTTGCATATTCTCTATAGTTG
EST: gi|124916010|gb|EH989884.1|EH989884
EST:     ATCCAGACAACACAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAGCCAAGTTGCTTGCATATTCTCTATAGTTG
genomic: ATCCAGACAACACAATGCGACAATTGCATAATTgtactctcat ... gtgtttgaagGGATTTATGTTCTGCCTCAGCCAAGTTGCTTGCATATTCTCTATAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATTgtactctcatactctctttttcttctacttttattggttttacacatgtgtgaaactaacaaatctcatcttgtgtgtttgaag

- - - - - - - - - - - - - - - - - - - - - - - -  AGGATG