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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAGTCCTTAAGATTCAACA

Basic information

species Arabidopsis thaliana
transcript AT2G43400.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 17
gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAGTCCTTAAGATTCAACA
           |  | | ||  |||    ||  |||     |||   |||    || || | ||  | |    |||  | ||||  |||  |  | | |            |||| ||||||||||||||||||||||| ||||| || ||||| || || |||||||| || || || |  ||  |  | |||||| |  ||  |    || 
----------gtatttgcctccatgttgattcagttgtc-catggacatttgcatcttttgtttcctgtaactgaa--tgaaat--gttgacggtatctgc----------agGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT

upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G032222_T02 (Zea mays), 3'ss of exon 17
gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAG--TCCTTAAGATTCAACA
 |  |     |||   |||||| |   | || | |  |   |   |   |  |  | |  | | |    |          ||  |  ||| ||| ||   | ||   | |  ||| || |||||||||||||||||||||||||| ||||||||||| || |||||||| || || ||||  ||  |  | ||||||  | || ||   | ||  
-tttgagcttcttag-gacttgctcttcctt-tctggagaaactccctcttttagcctctgctgggccat--------ccaagctaatttacttgttcactgtatcttca--gGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA--

upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 17
gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAGTCCT--TAAGATTCAACA
     ||| |     | |  |  |||   ||   | | | |||  |||  |  || |     ||| ||        | ||||     ||  |  || ||  ||| ||    |||| ||||| ||||||||||||||||| || || |||||||||||||||||||| ||||||||||| |  || ||  |||||||||| |  ||   ||||   
----ccattaggatgcaatgtcttgcttctttaataatactatacctacactagtaaagtctttgtttcctacccggtttaa-----ttcacacttgttcattattc----agGCTTGTGATATCAAAGATCCAAAGCAAAATATTGAGTGGACAGTGCCTGAAGGGGGTGGAGGCCCAGGATACTCAGTCATGTAGTCATGGTATTGTTCAC--

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|86087893|gb|DR383652.1|DR383652
EST:     AGGGTAAGCCAAAACTGCAGATCAACGCTCAAAACTGTTTGCACTGCAAG                         GCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAA
genomic: AGGGTAAGCCAAAACTGCAGATCAACGCTCAAAACTGTTTGCACTGCAAGgtacgcatca ... aatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAA
EST: gi|116411360|gb|EG453952.1|EG453952
EST:     AGGGTAAGCCAAAACTGCAGATCAACGCTCAAAACTGTTTGCACTGCAAG                         GCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAA
genomic: AGGGTAAGCCAAAACTGCAGATCAACGCTCAAAACTGTTTGCACTGCAAGgtacgcatca ... aatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAGTCCTTAAGATTCAACA
                                         ttttaat  putative branch site (score: 3)
                             ttttcttttttttttt  CT-rich tract
                    ttaaattggttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAGTCCTTAAGATTCAACA

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