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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgttaataccattgttgaaaactgattcagcatgatgactctggtaaacaattttgattgatgttttttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC

Basic information

species Arabidopsis thaliana
transcript AT3G48750.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 2
-----------gtatgatgttaatac-cattgttgaa-aactgattcagcatgatgactc---tggtaaacaattttgattgatgttttttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC
            | | |  ||  ||     ||||      || |||| || |  | | ||   |  | |   | ||   |||  ||| | ||    |||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| ||||| |||||||||||  |||| || ||    
tagccatgaaaatgttactttgctatgtgctgttcttcgtcttattctgcctttttagtcaattcattattgagttgctttgtggttgtgtggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTATCTGGACTTGGATCTAAAAAAACACATGGATTCATCTCCAGAGTTTGTG

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 2
-----gtatgatgttaat--accat-tgttgaa----aactgattcagca---tgatgactctggtaaacaattttgattgatgttt-tttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC
       |  ||||||||   |  | || ||        || |||| ||    |  | | |    ||   | || || ||| || || | ||    |||| ||||||||||| || ||||| ||||| || ||||||||||||||||||||||| ||||||||||| || || || ||||||||  |||| || ||    
ggccatgaaaatgttaatttgctgtgtgctgttcttcctcttattctgccttttagtcaattcattattgagttatgcttggtggttgtgtggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTATCTGGACTTGGATCTAAAGAAACATATGGATTCATCTCCAGAGTTTGTG

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 1
---gtatgatgttaataccattgttgaaaac-----tgattcagcatgatgactctggtaaaca-------attttgattgatgttt-tttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC
     || |||||  | |  ||  |  | ||     ||    |   | ||   |||  ||  ||       ||| | |||| ||| | | ||  || ||| ||||||||||| ||||||   |||||  |||||||||||||||||||||| |||||||| ||||| || ||||||||||||||  |||| || ||  | 
ctttaattatgttgcttcatttagttcatacattgttgtcctaatgttatttgtctcttagtcatttcctcattatcattggtgtatgtgtggaacgcagGTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTACCTTGACTTAGATCTAAAGAAGCACATGGATTCATCTCCAGAATTTGCA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 2
--gtatgatgttaataccatt------gttgaaaactgattcagcatgatgactctggtaaaca-------attttgattgatgttt-tttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC
   |||| || |     ||||      ||  |    ||    |   | ||   |||  ||| ||       ||| |  ||| ||| | | ||   ||||| ||||||||||| || ||    |||||  |||||||||||||||||||||| |||||||| ||||| || ||||||||||||||  |||| || ||  | 
aattatgttgcttgcttcatttagtctgtacattgttgtcctaatgttatttatctcttaatcatttcctcattatcgttggtgtatgtgtggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTACCTTGACTTAGATCTAAAGAAGCACATGGATTCATCTCCAGAATTTGCA

upper sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtatgatgttaataccattgttgaaaa---ctgattcagcatgatgactctggtaaacaattttgattgatgttttttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC
               | |  | ||  ||    |  | ||     ||  ||||   |    ||| |     | ||  |   ||||| | | |||    ||||  | |||||||| |||||||| ||||| || || ||||| |||||||||||||| ||||||||||| || ||||||||||||||  |||| |||||  ||
aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaat-atttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC

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|301501515|gb|HO207055.1|HO207055
EST:     ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAA                         ATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTA
genomic: ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgtt ... tgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTA
EST: gi|86036711|gb|DR332466.1|DR332466
EST:     ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCATAGCAACATTGTCAA                         ATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGGTTTTTGAGT
genomic: ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgtt ... tgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGG-TTTTTGAGT
EST: gi|163979562|gb|ES021829.1|ES021829
EST:     AGAGAAATCTCCCTCTTGAAAGAAATGCAGCATAGCAACATTGTCAA                         ATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTT
genomic: AGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgtt ... tgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTT
EST: gi|124717652|gb|EH809054.1|EH809054
EST:     AGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAA                         ATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGG
genomic: AGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgtt ... tgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGG
EST: gi|86036710|gb|DR332465.1|DR332465
EST:     ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCATAGCAACATTGTCAA                         ATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTA
genomic: ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgtt ... tgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTA
EST: gi|86036709|gb|DR332462.1|DR332462
EST:     ATCAGAGAAATCTCCCTCTTGAAAGARATGCAGCATAGCAACATTGTCAA                         AATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGGAG
genomic: ATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgtt ... tgctacacagA-TTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTG-AG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcagcatgatgactctggtaaacaattttgattgatgttttttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC
                                        ttttttgct  CT-rich tract
                     taaacaattttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgttaataccattgttgaaaactgattcagcatgatgactctggtaaacaattttgattgatgttttttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA