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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgctaaaccatactgtttgcgttagcttatatgacttagacttgtcttccgaaggccatttggcatcaaaatttagagatttcgagttctattttcagGGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTTTGGAGATTGTCATCTCTCCCTTGCC

Basic information

species Arabidopsis thaliana
transcript AT1G09795.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09795.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G33360.1 (Glycine max), 3'ss of exon 3
attgctaaaccatactgtttgcgttagcttatatgacttagacttgt-cttccgaaggccatttggcatcaaa--atttagagatttcgagttctattttcagGGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTTTGGAGATTGTCATCTCTCCCTTGCC
                ||  || ||  |  || ||    ||| | || |  | |           |  |||||   |||     | |    |||| || | |||| | |||||||||||||||||||||||| |||||| | | ||| ||||| | | | |||||||| 
----------------gtcagcattttcgcatttg---cagattagtgcccctgtgtattcgccagactcaaattgttttatcgtctaattttcttttgttagGGTAGTGAAGATCTTATCATTGTCCACGAGGCTCTCGAGTATGGTGATTGCCGTTTATCCCTTGCG

upper sequence: AT1G09795.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G36070.1 (Glycine max), 3'ss of exon 3
attgctaaaccatactgtttgcgttagcttatatgacttagacttgtcttccgaaggccatttggcatcaaaatttagagatt-tcgagttctatttt--cagGGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTTTGGAGATTGTCATCTCTCCCTTGCC
 ||||    |      ||||    |   ||  | |||| |          ||   |       | ||   || |||   |||  || | || | ||||   |||| ||||| |||||||||||||||||||| |||||  | | ||| ||||| | | | |||||||| 
-ttgccttgcttctgagttta-actgcattgca-gactaatgtcctagacccagtgtattcgcgacactcaatttttttgatcgtctaattttcttttgttagGGTAATGATGATCTTATCATTGTCCACGAGGCTCTGGAGTATGGTGATTGCCGTTTATCCCTTGCG
















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|125310272|gb|EL324357.1|EL324357
EST:     ATCTGGATCTGGGCATCGTTGGTCTTGACATAGTTGGTGAATTTGGTCAG                         GGAAATGAAGATCTTATCAT
genomic: ATCTGGATCTAGGCATCGTTGGTCTTGACATAGTTGGTGAATTTGGTCAGgtaaatgaca ... ctattttcagGGAAATGAAGATCTTATCAT
EST: gi|125046229|gb|EL118498.1|EL118498
EST:     GGTGAATTTGGTCAG                         GGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTT-GGAGATTGT
genomic: GGTGAATTTGGTCAGgtaaatgaca ... ctattttcagGGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTTTGGAGATTGT
EST: gi|125255934|gb|EL270019.1|EL270019
EST:     ATCTGGATCTAGGCATCGTTGGTCTTGACATAGTTGGTGAATTTGGTCAG                         GGAAATGAAGATCTTATCATTGTCC
genomic: ATCTGGATCTAGGCATCGTTGGTCTTGACATAGTTGGTGAATTTGGTCAGgtaaatgaca ... ctattttcagGGAAATGAAGATCTTATCATTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttccgaaggccatttggcatcaaaatttagagatttcgagttctattttcagGGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTTTGGAGATTGTCATCTCTCCCTTGCC
                                           ttctattttc  CT-rich tract
                        aaaatttagagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgctaaaccatactgtttgcgttagcttatatgacttagacttgtcttccgaaggccatttggcatcaaaatttagagatttcgagttctattttcagGGAAATGAAGATCTTATCATTGTCCACGAAGCTCTCAACTTTGGAGATTGTCATCTCTCCCTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcaaa