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

...aagatattttctacatggaatcctggttctgtcagaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA

Basic information

species Arabidopsis thaliana
transcript AT2G21410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 6
----aagatattttctacatggaatcctggttctgtc-agaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
    ||| |||||| || ||    | ||  | ||||| ||  |  |  |  |  |  | ||||      ||   | |   | ||   | ||   | ||   ||||| ||  ||||||| ||||||  | ||||| |||||||| |||||||||  ||||||||| ||||||||||| || ||    || |||||||| || ||  
gatgaagttattttttatatatcttact--tcctgtctagtcatgaagttattttattatttgttccaactctaagtcttcattctttgta---tgataacacagGTTGCCAAAAATGCATTTGTTATTTTCTACTCTGGGGATAGAGCAAAAGCCAAAATTCTGAAGATATGTGATGCGTTCAACGCAAATCGCTACCCATTTC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 6
-aagatattttctacatggaatcctg-gttctgtcagaaaaaat-atactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgtta--cagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
  |  |||   | |||   | || |  |||||  |   ||   | ||  | |||||  |||| |   ||   |  |  ||    | ||    ||  ||||  ||||    |||||||| ||||||| | ||||| ||||| || |||||||||| ||||||||| ||||||||||| || |||   || || || || || ||  
ccatttatcagc-acactaagtcttctgttctaactttaagtttgatgtttattct--ttgcttgaactt--atctatctgccaaccttttgtatggttatgcagGTAACGAAAAATGCATTTGTCATATTCTACTCTGGAGAGAGAGCAAAAACCAAAATTCTGAAGATATGTGATGCCTTTAATGCGAACCGTTACCCGTTTC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 6
aagatattttcta--catggaatcctggt--tctgtcagaaaaaatatactcattctgttt--gcctttgctagga-attgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
   || ||||||     |||||  ||  |  ||| |    |  | | ||||  | |||| |    ||||  |||   ||  | |  |   ||   |   | ||||||| | | |||||||||||||| ||||| |||||||| |||||||  |||||||||||||| || |||||||| |||||||| || ||||| ||||||||| 
---attttttctgattctggaaatctactcttctattgctactagt-tacttctactgtcttgatcttttttagttcataaagtcatagcct---ccctttttacagGTTCATAAAAATGTATTTGTTGTCTTTTATTCTGGAGAAAGAGTTAAAAGCAAAATTCTGAAAATATGTGATGCTTTTGGAGCAAATCGTTATCCTTTCT

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 6
aagatattt---tctacatggaatcctggttctgtcagaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
 ||||  ||   | |   | |||      |||||   |   | ||||| |  ||  | ||   | | |||     |||   || ||  |   | |   | ||| ||||||||||||| ||||| ||||||||| |||| |||| |||||||  ||| ||||| || ||||||||||| ||||| || ||||| || |||||  
gagattcttcatttttggttgaaataaatttctgcttgttgacatatatt--tttcggttttatattctatcctatgatgatttatggatgttcac-ctgcagACTGAGAAAAATGTTTTTGTGGTCTTCTATGCTGGTGAAAAAGCAAAAGCCAAGATTCTGAAAATATGTGAAGCCTTTGGTGCTAATCGTTACCCTTTTG

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 6
aagatattt---tctacatggaatcctggttctgtcagaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
 ||||  ||   | |  || |||      ||||| | |   | || || |  ||||||||    || |||     ||||  || |   |   | |   | ||| ||||||||||||| ||||| ||||||||| |||| |||| |||||||   || ||||| || ||||||||||| ||||| || ||||| || |||||  
tagattcttcatttttgattgaaataaatttctgcctgttgacatttattt-ttctgttttatatt-ctattctatgacgatttactgatgttcac-ctgcagACTGAGAAAAATGTTTTTGTGGTCTTCTATGCTGGTGAAAAAGCAAAAGCTAAGATTCTGAAAATATGTGAAGCCTTTGGTGCTAATCGTTACCCTTTTG

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 6
-----aagatattttctacatggaatcctggttctgtcagaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
     || ||    |  |||   |       |||| ||    ||  |||  || || | |      ||  ||     ||| || | |   |  | ||  |  |||   ||||||||||||||||| || ||||| ||||| |||| ||  || | |||||||||||||||||||||||||||||| || ||||||||  ||||  
taatgaacatgcacttaacactcacaatccattct-tctttcaatgtattttctttatatacttggttcttaatctctgagttgtaa---atcccaacat-gcagATCGAGAAAAATGTATTTGTGGTTTTCTACTCTGGAGAAAAAGTGAAGAACAAAATTCTTAAGATATGTGAAGCTTTTGGAGCAAATCGCTACTCTTTTC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S60_200V6.1 (Physcomitrella patens), 3'ss of exon 5
--aagatattttctacatggaatcctggttctgtcagaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
  |   | |||| ||    |     |      ||  |     |||||   ||      ||   ||  |   |  |||||| ||         ||   ||||| | |||||||  || ||||| || |||| |||||| ||  | || |||  |||  || | || || ||||| ||||||||||||||||||||||| ||| 
ctattgtgttttgtaataagtcaattatagtagtaggcttttatataaagatcagagatgatgttctttccatctgacttgtggaactggtcaaa--tacagACAGAGAAAACGGTCTTTGTTGTGTTCTTTTCTGGAGAGCGTGCCAAATCCAAGGTTGTCAAAATCTGTGAGGCTTTTGGGGCCAATCGCTATCCCTTCC

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|116483494|gb|EG526086.1|EG526086
EST:     GACAGTCTGTCATTGAGGAGTCTGTTGTTGATCCCAACTCTGGGGAGAAG                         GCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGC
genomic: GACAGTCTGTCATTGAGGAGTCTGTTGTTGATCCCAACTCTGGGGAGAAGgttagttgct ... aatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGC
EST: gi|125278930|gb|EL293015.1|EL293015
EST:     TCTGTCATTGAGGAGTCTGTTGTTGATCCCAACTCTGGGGAGAAG                         GCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGC
genomic: TCTGTCATTGAGGAGTCTGTTGTTGATCCCAACTCTGGGGAGAAGgttagttgct ... aatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA
                                         aactaat  putative branch site (score: 2)
                                       taaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatattttctacatggaatcctggttctgtcagaaaaaatatactcattctgtttgcctttgctaggaattgacttttgatctaaactaatgttacagGCTGAGAAAAATGTATTTGTCGTCTTCTATTCTGGGGAAAGAGCAAAAAGCAAAATTCTTAAGATATGTGAAGCTTTTGGGGCCAATCGCTATCCTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaact